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Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north‐western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre‐adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate. [ABSTRACT FROM AUTHOR]

Aim: Several large‐mammal species in Europe have recovered and recolonized parts of their historical ranges. Knowing where suitable habitat exists, and thus where range expansions are possible, is important for proactively promoting coexistence between people and large mammals in shared landscapes. We aimed to assess the opportunities and limitations for range expansions of Europe's two largest herbivores, the European bison (Bison bonasus) and moose (Alces alces). Location: Central Europe. Methods: We used large occurrence datasets from multiple populations and species distribution models to map environmentally suitable habitats for European bison and moose across Central Europe, and to assess human pressure inside the potential habitat. We then used circuit theory modeling to identify potential recolonization corridors. Results: We found widespread suitable habitats for both European bison (>120,000 km2) and moose (>244,000 km2), suggesting substantial potential for range expansions. However, much habitat was associated with high human pressure (37% and 43% for European bison and moose, respectively), particularly in the west of Central Europe. We identified a strong east–west gradient of decreasing connectivity, with major barriers likely limiting natural recolonization in many areas. Main conclusions: We identify major potential for restoring large herbivores and their functional roles in Europe's landscapes. However, we also highlight considerable challenges for conservation planning and wildlife management, including areas where recolonization likely leads to human–wildlife conflict and where barriers to movement prevent natural range expansion. Conservation measures restoring broad‐scale connectivity are needed in order to allow European bison and moose to recolonize their historical ranges. Finally, our analyses and maps indicate suitable but isolated habitat patches that are unlikely to be colonized but are candidate locations for reintroductions to establish reservoir populations. More generally, our work emphasizes that transboundary cooperation is needed for restoring large herbivores and their ecological roles, and to foster coexistence with people in Europe's landscapes. [ABSTRACT FROM AUTHOR]

Aim: Genome‐wide genetic data can provide key input for both taxonomy and conservation, but its use in this context remains limited. In this study, we performed the first genome‐wide assessment of genetic variation in two populations of the Eurasian lynx, the Balkan population, the most threatened, and the Caucasian population, a possible glacial refugium, with the aim to place them in the context of the species, investigate their demographic history and evaluate their genetic status. Location: The Balkans and the Caucasus. Methods: We obtained whole genome resequencing data from seven Balkan and 12 Caucasian lynx, and analysed them along with novel and existing data from other populations. Based on a total 105 whole genome and 114 mitogenome sequences, we reconstructed phylogenetic and historical relationships, ancient and recent demography, and patterns of genetic diversity and inbreeding. Results: Both the Balkan and the Caucasian lynx appear as distinct mitochondrial lineages that diverged from the rest of the Eurasian lynx lineages ca. 92.6 kya, and from each other ca. 46.4 kya. Autosomal data suggest, however, that the Balkan lynx is closely related with the Carpathian population, and revealing alarmingly low genetic diversity and high inbreeding. In contrast, the Caucasian lynx shows a longer history of relative isolation from the rest of lynx populations and high genetic diversity, consistent with its large long‐term effective population size. Main conclusions: The taxonomic status of the Balkan lynx remains unresolved due to the evidence of long‐term isolation in the mitogenome, contrasting with extensive autosomal admixture and intense recent genetic drift in the nuclear genome. Our results alert on genetic risks and call for the consideration of genetic rescue from closely related Carpathian lynxes. In contrast, substantial mitogenomic and autosomal divergence with no signs of genetic drift supports the identification of the Caucasian lynx as a separate subspecies with good genetic health. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. This study is focused on genetic differentiation among two transboundary Carpathian brown bear populations subjected to different conservation/management. We obtained results that are coherent for mitochondrial DNA and microsatellites, unveiling significant differentiation which is homogenized to some extent by male‐biased gene flow. These results can be implemented in a joint Carpathian brown bear management plan, pointing to retention of population connectivity via the Carpathian migratory corridor. [ABSTRACT FROM AUTHOR]

The exo,anti/exo,syn-diastereoselectivity of water promoted direct aldol reactions of tropinone and granatanone (pseudopelletierine) is strongly dependent on the amount of water added and aromatic aldehyde used. DFT methods were applied to calculate the free energies of tropinone and granatanone enols, transition states, and isomeric aldol products. A theoretical model was verified by comparison of results from several DFT methods and functionals with experiments. The 6-31g(d)/CPCM method proved most suited to the problem, although all methods tested predicted similar trends. Explicit inclusion of a water molecule bonded to the amino ketones resulted in increased stability of the enol forms. The dependence of the anti/syn-diastereoselectivity on the amount of water used may be rationalized on the basis of change in the polarity of the reaction medium. The predicted stabilities of competing products agreed with experimental results supporting the notion of thermodynamic control. The isomeric products distributions for the aldol reaction of several aromatic aldehydes in solventless (neat) conditions were accurately calculated from free energies of the aldol addition step in the gas phase using B3LYP/6-31g(d) method and in aqueous conditions using the CPCM-B3LYP/6-31g(d) model. Our methodology can be useful for predicting the outcome of this type of aldol reactions. [ABSTRACT FROM AUTHOR]

We analysed the genetic structure of 33 populations of the root vole (tundra vole, Microtus oeconomus, Pallas, 1776) inhabiting their typical habitats, located at different distances from the southern boundary of the species' range (52°14′-53°56′ N) in eastern Poland. We determined its phylogeographic pattern as well as the possible occurrence of a small, local high-latitude refugium of this species in southern Poland, previously suggested in palaeontological studies. 908 bp of cytochrome b sequences were analysed from 439 root voles, and 21 mt DNA cytb haplotypes belonging to the Central European ( CE) phylogroup were found. Haplotype diversity in the examined populations varied between 0 and 0.872 (mean: 0.425 ± 0.332), while nucleotide diversity ranged between 0 and 0.62% (mean: 0.235% ± 0.217). Within the CE phylogroup of M. oeconomus, we identified with high bootstrap support a newly separated group of M. oeconomus that evolved from CE, denoted CE- PL S. This group is located in the southern and central part of eastern Poland and most likely diverged from phylogroup CE in a small, cryptic refugium situated in southern Poland, in the Kraków- Częstochowa Upland and/or the Holy Cross Mountains during the LGM and Younger Dryas. [ABSTRACT FROM AUTHOR]

Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer ( Capreolus capreolus) in Poland from mitochondrial ( CR and cyt b) and sex-linked markers ( ZFX, SRY, DBY4 and DBY8). Analyses of CR mt DNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer ( C. pygargus) mt DNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mt DNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8-10.0 ka BP). Initially, introgressed mt DNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mt DNA introgression. [ABSTRACT FROM AUTHOR]

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 < 0.001, F ST = 0.464, P < 0.001)]. Spatial Analysis of Molecular Variance identified four separate groups of populations: (1) Norway, Finland and Estonia; (2) Latvia and North Eastern Poland; (3) the Białowieża Primeval Forest; (4) the Carpathians. The patterns of genetic diversity and differentiation suggested a number of discrete populations that are poorly connected by contemporary gene flow and could therefore be considered demographically independent. The peripheral location of these populations, habitat fragmentation and the strict territorial structure of lynx populations are factors likely contributing to the observed patterns. The study provides suggestions for active conservation/management decisions including translocations or reintroductions of lynx. [ABSTRACT FROM AUTHOR]

. 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. [ABSTRACT FROM AUTHOR]

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. 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. A 373-bp-long mtDNA control region fragment was amplified from 276 feral and 166 ranch mink. 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. 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. [ABSTRACT FROM AUTHOR]

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 + H. 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 [ABSTRACT FROM AUTHOR]

This paper presents an application of the reaction class transition state theory (RC-TST) to predict thermal rate constants for the hydrogen abstraction R&bond;OH + H → R&bond;O• + 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 [ABSTRACT FROM AUTHOR]

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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. [ABSTRACT FROM AUTHOR]

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 [ABSTRACT FROM AUTHOR]

Abstract 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 (F ST = 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 (H O = 0.111) values and the highest F IS ( 0.380), when compared to other two populations (G/N = 0.26–0.27, H O = 0.166–178, F IS = 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 . [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Review: 96 refs. [ABSTRACT FROM AUTHOR]