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Lucena-Pérez, María et al., Disentangling the contribution of long‐term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long‐term isolation and/or more recent human‐driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long‐term isolation argue for the restoration of lost population connectivity.

The abundance and distribution of large carnivores in Europe have been historically reduced. Their recovery requires multilevel coordination, especially regarding transboundary populations. Here, we apply nuclear and mitochondrial genetic markers to test for admixture level and its impact on population genetic structure of contemporary brown bears (Ursus arctos) from the Eastern, Southern, and Western Carpathians. Carpathian Mountains (Europe). Nearly 400 noninvasive brown bear DNA samples from the Western (Poland) and Eastern Carpathians (Bieszczady Mountains in Poland, Slovakia, Ukraine) were collected. Together with DNA isolates from Slovakia and Romania, they were analyzed using the set of eight microsatellite loci and two mtDNA regions (control region and cytochrome b). A set of 113 individuals with complete genotypes was used to investigate genetic differentiation across national boundaries, genetic structuring within and between populations, and movement between populations. Transboundary brown bear subpopulations (Slovakia and Poland) did not show significant internal genetic structure, and thus were treated as cohesive units. All brown bears from the Western Carpathians carried mitochondrial haplotypes from the Eastern lineage, while the Western lineage prevailed in the brown bears from the Bieszczady Mountains. Despite similar levels of microsatellite variability, we documented significant differentiation among the studied populations for nuclear markers and mtDNA. We also detected male‐biased and asymmetrical movement into the Bieszczady Mountains population from the Western Carpathians. Our findings suggest initial colonization of the Western Carpathians by brown bears possessing mtDNA from the Eastern lineage. Genetic structuring among populations at microsatellite loci could be a result of human‐mediated alterations. Detected asymmetric gene flow suggests ongoing expansion from more abundant populations into the Bieszczady Mountains and thus supports a metapopulation model. The knowledge concerning this complex pattern can be implemented in a joint Carpathian brown bear management plan that should allow population mixing by dispersing males.

Performance of the Reaction Class Transition State Theory (RC-TST) for prediction of rates constants of elementary reactions is examined using data from its previous applications to a number of different reaction classes. The RC-TST theory is taking advantage of the common structure denominator of all reactions in a given family combined with structure activity relationships to provide a rigorous theoretical framework to obtain rate expression of any reaction within a reaction class in a simple and cost-effective manner. This opens the possibility for integrating this methodology with an automated mechanism generator for “on-the-fly” generation of accurate kinetic models of complex reacting systems.

Large terrestrial carnivores are particularly prone to factors constraining levels of population genetic diversity because of their low densities and high spatial requirements. We studied the pattern of Eurasian lynx Lynx lynx population genetic variability in the westernmost part of its natural range from Scandinavia to the Carpathian Mountains (north-central Europe) based on 190 samples using 613 base pair-long sequences from the mitochondrial DNA control region (mtDNA-cr). We examined whether the population history or contemporary habitat constraints of this large and mobile carnivore could have significantly affected its genetic structure. We recorded nine mtDNA haplotypes, including five not previously reported. Lynx from Latvia and Estonia had the highest variability with haplotype and nucleotide diversities of 0.81–0.88% and 0.44–0.47%, respectively. In contrast, there was no polymorphism present in peripheral populations from Norway and the Carpathian Mountains. Lynx populations were strongly differentiated [analysis of molecular variance (AMOVA): Φ ST = 0.570, P

Chromosomal rearrangements are proposed to promote genetic differentiation between chromosomally differentiated taxa and therefore promote speciation. Due to their remarkable karyotypic polymorphism, the shrews of the Sorex araneus group were used to investigate the impact of chromosomal rearrangements on gene flow. Five intraspecific chromosomal hybrid zones characterized by different levels of karyotypic complexity were studied using 16 microsatellites markers. We observed low levels of genetic differentiation even in the hybrid zones with the highest karyotypic complexity. No evidence of restricted gene flow between differently rearranged chromosomes was observed. Contrary to what was observed at the interspecific level, the effect of chromosomal rearrangements on gene flow was undetectable within the S. araneus species.

1. The endangered butterfly Phengaris alcon exists in two ecotypes (P. ‘alcon’ and P. ‘rebeli’), which inhabit contrasting biotopes (wet and warm/dry grasslands respectively) and use different larval food plants. The initially flower-bud-feeding caterpillars complete their development as social parasites of Myrmica ants, and the specificity of these relationships shows geographical variation. 2. We studied the genetic structure of 16 populations (365 individuals) of both ecotypes in eastern Europe, sampling P. ‘rebeli’ in two disjunct areas in Lithuania and southern Poland, and P. ‘alcon’ on Polish localities between them. We analysed the cytochrome c oxidase subunit I (COI) mitochondrial gene, the EF1-α nuclear gene and five polymorphic microsatellite loci. 3. All individuals shared an identical COI haplotype, which we hypothesise may be linked to a selective sweep associated with the presence of the Wolbachia B strain in all populations. 4. For nuclear markers, we did not find a clear pattern reflecting division into two putative ecotypes. However, ecotypes differed significantly in their genetic variability, i.e., the P. ‘rebeli’ ecotype was less polymorphic, and its populations were much more differentiated (FST: 0.632 for EF1-α and 0.504 for microsatellites) than the P. ‘alcon’ ecotype (0.177 and 0.082, respectively). 5. Our microsatellite data suggest that all populations of P. ‘alcon’ form a single clade but that P ‘rebeli’ can be split into either six or two clades. The former model would indicate many independent origins, especially in the mountainous areas of southern Poland. The latter, not mutually exclusive, grouping clearly reflects the use of different host ants.

Aim Invasive alien species usually exhibit very high adaptation and rapid evolution in a new environment, but they often have low levels of genetic diversity (invasive species paradox). Genetic variation and population genetic structure of feral American mink, Neovison vison, in Poland was investigated to explain the invasion paradox and to assess current gene flow. Furthermore, the influence of mink farming on adaptation of the feral population was evaluated by comparing the genetic structure of feral and ranch mink. Location Samples from feral mink were collected in 11 study areas in northern and central Poland and from ranch mink at 10 farms distributed throughout the country. Methods A 373-bp-long mtDNA control region fragment was amplified from 276 feral and 166 ranch mink. Results Overall, 31 haplotypes, belonging to two groups from genetically diverse sources, were detected: 11 only in feral mink, 12 only in ranch mink and eight in both. The genetic differentiation of feral mink from the trapping sites was high, while that among ranch mink from various farms was moderate. There was no significant relationship between genetic and geographic distance. The number of trapping sites where given haplotypes occurred correlated with the number of farms with these haplotypes. The mink from two sites were the most divergent, both from all other feral mink and from ranch mink. Comparison of mtDNA and microsatellite differentiation suggests male-biased dispersal in this species. Main conclusions American mink in Poland exhibit high genetic diversity and originate from different source populations of their native range. The process of colonization was triggered by numerous escapees from various farms and by immigrants from Belarus. The genetic structure of local feral mink populations was shaped by the founder effect and multiple introductions. The genomic admixture that occurred during mixing of different populations might have increased the fitness of individuals and accelerated the invasiveness of this species.

1 The Eurasian lynx Lynx lynx occupies a variety of environmental and climatic conditions, and the majority of present-day European populations have either recovered from severe demographic bottlenecks, or are living in fragmented habitat. These factors may have affected the genetic variability of lynx populations. We summarize available data on genetics, population status and ecology of these felids to shed light on the pattern and mechanisms behind their genetic variability and population differentiation in Europe. 2 Genetic studies conducted so far, based on mtDNA and microsatellites, have shown that the Eurasian lynx has low to moderate genetic variability. Variability is lowest in the north (Scandinavian bottlenecked population), but is also low in the Carpathian region. A trend towards loss of genetic variation has been noted in fragmented and reintroduced populations. Genetically, the populations are highly differentiated from each other. 3 There are clear relationships between the pattern of lynx genetic variability, differentiation between the populations, and such factors as population history (demographic bottlenecks), social interactions and habitat fragmentation. The genetic divergence between lynx populations is also strongly correlated with the depth and duration of snow cover. 4 Our review provides evidence that the lynx is undergoing significant genetic differentiation, due to several factors. To enable better planning of conservation programmes for the Eurasian lynx, researchers should identify the Evolutionarily Significant Units among its populations, using different classes of molecular markers.

This paper presents an application of the reaction class transition state theory (RC-TST) to predict thermal rate constants for hydrogen abstraction reactions of the type R-OH + H R•-OH + H2. We have derived all parameters for the RC-TST method with linear energy relationships (LERs) and the barrier height grouping (BHG) approach for this reaction class from rate constants of 37 representative reactions divided in two types of hydrogen abstraction, namely from α carbon sites and non-α carbon sites two training sets. Error analyses indicate that the RC-TST/LER, where only reaction energy is needed, and RC-TST/ BHG, where no other information is needed, can predict rate constants for any reaction in this reaction class with satisfactory accuracy for combustion modeling. Specifically for this reaction class, the RC-TST/LER and RC-TST/BHG methods have, respectively, less than 40% and 90% systematic errors in the predicted rate constants, when compared to the explicit full TST/Eckart method. The branching ratio analysis shows that in the low-temperature regime α abstractions are dominant, whereas, for T > 1500 K, abstractions at other sites become more important. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 43: 78–98, 2011

This paper presents an application of the reaction class transition state theory (RC-TST) to predict thermal rate constants for the hydrogen abstraction ROH + H RO• + H2 reaction class, where R is an alkyl group. We have derived all parameters for the RC-TST method for this reaction class from rate constants of 19 representative reactions, coupling with linear energy relationships (LERs) and the barrier height grouping (BHG) approach. Error analyses indicate that the RC-TST/LER, where only reaction energy is needed, and RC-TST/BHG, where no other information is needed, can predict rate constants for any reaction in this reaction class with satisfactory accuracy for combustion modeling. Specifically for this reaction class, the RC-TST/LER method has less than 25% systematic errors in the predicted rate constants, whereas the RC-TST/BHG method has less than 35% error when compared to explicit rate calculations. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 414–429, 2010

Behavioural ecologists have long been interested in mating systems and variance of reproductive success. Highly variable molecular markers now enable researchers to reassess mating systems from the genetic point of view. We used 10 microsatellite loci to detail the mating pattern and male reproductive success in a natural population of the common vole Microtus arvalis, one of the most numerous species in Europe. By genotyping 32 females and their offspring, we found evidence for multiple paternity in 50% of litters sired by two or three males. This result was confirmed by paternity analysis of candidate fathers caught in the population; it also showed that both males and females mated with several unrelated partners. Comparisons of two sires in a given multiple-sire litter showed their relatedness to be low. The common vole population was characterized by a relatively high standardized variance of male reproductive success, indicating that males competed for mating. While one of the males could sire up to 83% of offspring in a multiple-sire litter, mating with an already mated female gave lower reproductive success than mating with one female exclusively. Our results suggest that the occurrence of multiple paternity in the common vole population can be explained by the inability of males to monopolize and mate with all females of a colony, and also by their tendency to increase their reproductive success by getting access to already mated females.

Different aspects of the symbolic algebra computations for generating elementary reactions of complex systems are reviewed. Such calculations are the heart of each automated mechanism generator system and are employed extensively in different stages of mechanism generation. The range of symbolic calculation topics and basic ideas of these implementations, together with some specific examples, are given. Particular attention is devoted to the transition between the symbolic calculation and the real complex chemistry. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Three populations of the rare and endangered plant species Cypripedium calceolus were included in a study of genetic diversity and spatial genetic structure in the Biebrza National Park, northeast Poland. Analysis of 11 allozyme loci indicate that the populations of this species contained high genetic variability (P = 45.5%, A= 1.73). On the other hand, the genetic differentiation (FST = 0.014, P < 0.05) among C. calceolus populations was very low when compared to other species with similar life history characteristics. The observed high rate of gene flow (Nm = 18) may suggest that the populations studied derived from each other in the recent past. Five polymorphic allozyme markers identified 109 multilocus genotypes in three populations and the majority of them (67%) were population-specific. One of the populations studied, characterized by particularly extensive vegetative reproduction, showed the lowest clonal diversity (G/N = 0.15) and heterozygosity (HO = 0.111) values and the highest FIS(0.380), when compared to other two populations (G/N = 0.26-0.27, HO= 0.166-178, FIS = 0.024-0.055). This may indicate that clonal reproduction has an important influence on the genetic structure of C. calceolus populations. The longevity of genets, the out-crossing breeding system and the presence of recruitment from seeds are factors maintaining genetic diversity in C. calceolus.

We developed nine polymorphic microsatellite loci for the field vole, Microtus agrestis. The number of alleles ranged from five to 15 and observed heterozygosities ranged from 0.40 to 1.00. We also tested the microsatellite loci for amplification and polymorphism in the congeneric species Microtus arvalis. Five of the nine loci were successfully analysed in this species. The microsatellite markers will be employed in studies of reproductive success and fine-scale spatial genetic structure.