A Note on the Majority Dynamics in Inhomogeneous Random Graphs

In this note, we study discrete time majority dynamics over an inhomogeneous random graph G obtained by including each edge e in the complete graph $$K_n$$ K n independently with probability $$p_n(e)$$ p n ( e ) . Each vertex is independently assigned an initial state $$+1$$ + 1 (with probability $$p_+$$ p + ) or $$-1$$ - 1 (with probability $$1-p_+$$ 1 - p + ), updated at each time step following the majority of its neighbors’ states. Under some regularity and density conditions of the edge probability sequence, if $$p_+$$ p + is smaller than a threshold, then G will display a unanimous state $$-1$$ - 1 asymptotically almost surely, meaning that the probability of reaching consensus tends to one as $$n\rightarrow \infty $$ n → ∞ . The consensus reaching process has a clear difference in terms of the initial state assignment probability: In a dense random graph $$p_+$$ p + can be near a half, while in a sparse random graph $$p_+$$ p + has to be vanishing. The size of a dynamic monopoly in G is also discussed.

DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania

We aimed to extract DNA and amplify PCR fragments at the mitochondrial DNA Nad7.1 locus and 11 nuclear microsatellite loci in nine circa 11,000-year-old individuals of Scots pine found at the bottom of the Baltic sea and test the genetic associations with the present-day gene pool of Scots pine in Lithuania. We followed a strict anticontamination protocol in the lab and, simultaneously with the aDNA specimens, tested DNA-free controls. The DNA was extracted by an ATMAB protocol from the ancient wood specimens sampled underwater from Scots pine stumps located circa 20–30 m deep and circa 12 km ashore in western Lithuania. As the references, we used 30 present-day Lithuanian populations of Scots pine with 25–50 individuals each. The aDNA yield was 11–41 ng/μL. The PCR amplification for the mtDNA Nad7.1 locus and the nDNA loci yielded reliable aDNA fragments for three and seven out of nine ancient pines, respectively. The electrophoresis profiles of all the PCR tested DNA-free controls contained the sizing standard only, indicating low likelihood for contamination. At the mtDNA Nad7.1 locus, all three ancient Scots pine individuals had the type A (300 bp) allele, indicating postglacial migration from the refugia in Balkan peninsula. The GENECLASS Bayesian assignment tests revealed relatively stringer and consistent genetic associations between the ancient Scots pine trees and the present-day southern Lithuanian populations (assignment probability 0.37–0.55) and several wetlands in Lithuania. Our study shows that salty sea water efficiently preserves ancient DNA in wood at the quality levels suitable for genetic testing of trees dated back as far as 11,000 years before present.

Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus

Conservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear Helarctos malayanus. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability ≥ 85%), providing valuable information for future bear reintroduction programs. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.

Identifying the Harm of Manipulable School-Choice Mechanisms

An important but under-explored issue in student assignment procedures is heterogeneity in the level of strategic sophistication among students. Our work provides the first direct measure of which students rank schools following their true preference order (sincere students) and which rank schools by manipulating their true preferences (sophisticated students). We present evidence that our proxy for sophistication captures systematic differences among students. Our results demonstrate that sophisticated students are 9.6 percentage points more likely to be assigned to one of their preferred schools. Further, we show that this large difference in assignment probability occurs because sophisticated students systematically avoid over-demanded schools. (JEL D82, H75, I21, I28)

Population and individual identification of coho salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability <0.85 excluded from the analysis, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. A PBT–GSI or PBT system of identification will provide an alternate method of identification in the assessment and management of Canadian-origin coho salmon relative to the existing CWT program.

Analytical limits of hybrid identification using genetic markers: an empirical and simulation study in Hippolais warblers

Hybridization is known to occur in a wide range of avian species, yet the rate and persistence of hybridization on populations is often hard to assess. Genotyping using variable genetic marker sets has become a common tool to identify hybrid individuals, however assignment outputs can differ depending on the marker set used. Here, we study hybrid assignment in two sibling Hippolais warblers, where hybrid assignment has shown to differ between SSR and AFLP markers. Simulation of heterospecific individuals as well as backcrosses (typed using SSR markers) reveals a rapid loss of assignment probability in higher backcross generations. However, the characterization of F1 hybrids was clearly distinguished from both parental taxa. The differences in marker sets are not contradictory but complementary. The rate of hybridization is lower than previously expected with AFLP markers but introgression might be long-lasting. This could be either due to differences in power of the marker systems used or due to non-neutral variation covered by AFLP but not SSR markers. We call for more attention to be paid regarding the potential limits of classical marker systems to investigate hybridization and its persistence in natural systems.

Introgression in the genus Campylobacter: generation and spread of mosaic alleles

Horizontal genetic exchange strongly influences the evolution of many bacteria, substantially contributing to difficulties in defining their position in taxonomic groups. In particular, how clusters of related bacterial genotypes – currently classified as microbiological species – evolve and are maintained remains controversial. The nature and magnitude of gene exchange between two closely related (approx. 15 % nucleotide divergence) microbiologically defined species, Campylobacter jejuni and Campylobacter coli, was investigated by the examination of mosaic alleles, those with some ancestry from each population. A total of 1738 alleles from 2953 seven-locus housekeeping gene sequence types (STs) were probabilistically assigned to each species group with the model-based clustering algorithm structure. Alleles with less than 75 % assignment probability to one of the populations were confirmed as mosaics using the structure linkage model. For each of these, the putative source of the recombinant region was determined and the allele was mapped onto a clonalframe genealogy derived from concatenated ST sequences. This enabled the direction and frequency of introgression between the two populations to be established, with 8.3 % of C. coli clade 1 alleles having acquired C. jejuni sequence, compared to 0.5 % for the reciprocal process. Once generated, mosaic genes spread within C. coli clade 1 by a combination of clonal expansion and lateral gene transfer, with some evidence of erosion of the mosaics by reacquisition of C. coli sequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species.

Evaluation of the Variety of Plasmid Profiles inS epidermidisIsolates from Hospital Patients and Staff

Plasmid profiling was used to determine the variability of normal flora isolates ofStaphylococcus epidermidisin order to evaluate the usefulness of plasmid profiling for identifying pathogens. Fifteen hospital staff members and patients repeatedly had cultures taken from the hands and nares, and multiple isolates were examined for plasmid profiles.S epidermidisisolated from the nares of 15 neonates were also examined. The total number of isolates examined for plasmid profiles was 726. Repetition of profiles was common among the different isolates from a single sampling (one swab). The frequency of re-isolating similar profiles on different days varied from 7% to 13%. Simultaneous isolation of similar profiles from nares and hands on the same individual varied from 0% to 11%, the percentage being lower for personnel. Isolation of the same plasmid profile from different individuals occurred only twice and resulted in an assignment probability ofPa= 0.002 for isolates obtained from different individuals. Significantly more isolates from nares contained plasmids (97%) compared with isolates from hands (89%).Patients who had two or more isolates of coagulase-negative staphylococci with similar profiles were judged, clinically, to have infections in 12 of 13 cases. However, the likelihood of re-isolating anS epidermidisstrain with a similar plasmid profile twice from the same person at different times was sufficiently high to prevent plasmid profiling from being used as an absolute criterion for infection.