Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system

Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and decline worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout (Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia, and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked vs. not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in nonstocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contributes to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long‐term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems.     

Finding flies in the mushroom soup: Host specificity of fungus‐associated communities revisited with a novel molecular method

Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour‐intensive methods involving cultivation and morphology‐based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt–isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean‐up step using solid‐phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples—regardless of biomass or other properties—being successfully PCR‐amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus‐associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology‐based identifications, we find a species‐rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus‐associated interaction webs and communities. Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour‐intensive methods involving cultivation and morphology‐based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt–isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean‐up step using solid‐phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples—regardless of biomass or other properties—being successfully PCR‐amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus‐associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology‐based identifications, we find a species‐rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus‐associated interaction webs and communities.     

Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle

The Hymenoptera constitutes one of the largest, and ecologically and economically most important, insect orders. During the past decade, a number of hypotheses on the phylogenetic relationships among hymenopteran families and superfamilies have been presented, based on analyses of molecular and/or morphological data. Nevertheless, many questions still remain, particularly concerning relationships within the hyperdiverse suborder Apocrita, but also when it comes to the evolutionary history of the ancestrally herbivorous “sawfly” lineages that form the basal, paraphyletic grade Symphyta. Because a large part of the uncertainty appears to stem from limited molecular and taxonomic sampling, we set out to investigate the phylogeny of Hymenoptera using nine protein‐coding genes, of which five are new to analyses of the order. In addition, we more than tripled the taxon coverage across the symphytan grade, introducing representatives for many previously unsampled lineages. We recover a well supported phylogenetic structure for these early herbivorous hymenopteran clades, with new information regarding the monophyly of Xyelidae, the placement of the superfamily Pamphilioidea as sister to Tenthredinoidea + Unicalcarida, as well as the interrelationships among the tenthredinoid families Tenthredinidae, Cimbicidae, and Diprionidae. Based on the obtained phylogenies, and to prevent paraphyly of Tenthredinidae, we propose erection of the tribe Heptamelini to family status (Heptamelidae). In particular, our results give new insights into subfamilial relationships within the Tenthredinidae and other species‐rich sawfly families. The expanded gene set provides a useful toolbox for future detailed analyses of symphytan subgroups, especially within the diverse superfamily Tenthredinoidea.     

Polygenic impact of morningness on the overnight dynamics of sleep spindle amplitude

Sleep spindles are thalamocortical oscillations that contribute to sleep maintenance and sleep‐related brain plasticity. The current study is an explorative study of the circadian dynamics of sleep spindles in relation to a polygenic score (PGS) for circadian preference towards morningness. The participants represent the 17‐year follow‐up of a birth cohort having both genome‐wide data and an ambulatory sleep electroencephalography measurement available ( N = 154, Mean age = 16.9, SD = 0.1 years, 57% girls). Based on a recent genome‐wide association study, we calculated a PGS for circadian preference towards morningness across the whole genome, including 354 single‐nucleotide polymorphisms. Stage 2 slow (9‐12.5 Hz, N = 186 739) and fast (12.5‐16 Hz, N = 135 504) sleep spindles were detected using an automated algorithm with individual time tags and amplitudes for each spindle. There was a significant interaction of PGS for morningness and timing of sleep spindles across the night. These growth curve models showed a curvilinear trajectory of spindle amplitudes: those with a higher PGS for morningness showed higher slow spindle amplitudes in frontal derivations, and a faster dissipation of spindle amplitude in central derivations. Overall, the findings provide new evidence on how individual sleep spindle trajectories are influenced by genetic factors associated with circadian type. The finding may lead to new hypotheses on the associations previously observed between circadian types, psychiatric problems and spindle activity.     

4D prediction of protein <Superscript>1</Superscript>H chemical shifts

A 4D approach for protein ¹H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6–7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins the RMS errors were 0.17–0.34 and 0.34–0.65 ppm for the Hα and HN shifts, respectively. X-ray structures gave better predictions than the corresponding NMR structures, indicating that chemical shifts contain invaluable information about local structures. The ¹H chemical shift prediction tool 4DSPOT is available from .     

A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation

Sex hormone-binding globulin (SHBG) is a glycoprotein responsible for the transport and biologic availability of sex steroid hormones, primarily testosterone and estradiol. SHBG has been associated with chronic diseases including type 2 diabetes (T2D) and with hormone-sensitive cancers such as breast and prostate cancer. We performed a genome-wide association study (GWAS) meta-analysis of 21,791 individuals from 10 epidemiologic studies and validated these findings in 7,046 individuals in an additional six studies. We identified twelve genomic regions (SNPs) associated with circulating SHBG concentrations. Loci near the identified SNPs included SHBG (rs12150660, 17p13.1, p = 1.8 × 10(-106)), PRMT6 (rs17496332, 1p13.3, p = 1.4 × 10(-11)), GCKR (rs780093, 2p23.3, p = 2.2 × 10(-16)), ZBTB10 (rs440837, 8q21.13, p = 3.4 × 10(-09)), JMJD1C (rs7910927, 10q21.3, p = 6.1 × 10(-35)), SLCO1B1 (rs4149056, 12p12.1, p = 1.9 × 10(-08)), NR2F2 (rs8023580, 15q26.2, p = 8.3 × 10(-12)), ZNF652 (rs2411984, 17q21.32, p = 3.5 × 10(-14)), TDGF3 (rs1573036, Xq22.3, p = 4.1 × 10(-14)), LHCGR (rs10454142, 2p16.3, p = 1.3 × 10(-07)), BAIAP2L1 (rs3779195, 7q21.3, p = 2.7 × 10(-08)), and UGT2B15 (rs293428, 4q13.2, p = 5.5 × 10(-06)). These genes encompass multiple biologic pathways, including hepatic function, lipid metabolism, carbohydrate metabolism and T2D, androgen and estrogen receptor function, epigenetic effects, and the biology of sex steroid hormone-responsive cancers including breast and prostate cancer. We found evidence of sex-differentiated genetic influences on SHBG. In a sex-specific GWAS, the loci 4q13.2-UGT2B15 was significant in men only (men p = 2.5 × 10(-08), women p = 0.66, heterogeneity p = 0.003). Additionally, three loci showed strong sex-differentiated effects: 17p13.1-SHBG and Xq22.3-TDGF3 were stronger in men, whereas 8q21.12-ZBTB10 was stronger in women. Conditional analyses identified additional signals at the SHBG gene that together almost double the proportion of variance explained at the locus. Using an independent study of 1,129 individuals, all SNPs identified in the overall or sex-differentiated or conditional analyses explained ~15.6% and ~8.4% of the genetic variation of SHBG concentrations in men and women, respectively. The evidence for sex-differentiated effects and allelic heterogeneity highlight the importance of considering these features when estimating complex trait variance.     

Castrating parasites and colonial hosts

Trajectories of life-history traits such as growth and reproduction generally level off with age and increasing size. However, colonial animals may exhibit indefinite, exponential growth via modular iteration thus providing a long-lived host source for parasite exploitation. In addition, modular iteration entails a lack of germ line sequestration. Castration of such hosts by parasites may therefore be impermanent or precluded, unlike the general case for unitary animal hosts. Despite these intriguing correlates of coloniality, patterns of colonial host exploitation have not been well studied. We examined these patterns by characterizing the responses of a myxozoan endoparasite, Tetracapsuloides bryosalmonae, and its colonial bryozoan host, Fredericella sultana, to 3 different resource levels. We show that (1) the development of infectious stages nearly always castrates colonies regardless of host condition, (2) castration reduces partial mortality and (3) development of transmission stages is resource-mediated. Unlike familiar castrator-host systems, this system appears to be characterized by periodic rather than permanent castration. Periodic castration may be permitted by 2 key life history traits: developmental cycling of the parasite between quiescent (covert infections) and virulent infectious stages (overt infections) and the absence of germ line sequestration which allows host reproduction in between bouts of castration.     

Larval parasitism rate increases in herbivore‐damaged trees: a field experiment with cyclic birch feeding moths

Indirect plant defence mechanisms enhance the effectiveness of natural enemies of herbivores. Herbivore‐induced plant volatiles (HIPVs) attract the parasitoids of insect herbivores as shown both in numerous choice tests conducted under laboratory conditions and in relatively few common‐garden setups in agro‐ecosystems. However, the importance of this indirect defence trait at higher levels of biological organization has yet to be investigated through natural field experiments. Here, we report a field experiment of larval parasitism of two cyclic geometrid defoliators in herbivore‐damaged and fairly intact mountain birch Betula pubescens ssp. czerepanovii under natural conditions. Parasitism rates in larvae of the autumnal (Epirrita autumnata) and winter moth (Operophtera brumata) exposed for 30 h on defoliated trees were more than twice as high as those on control trees. This finding indicates that hymenopteran parasitoids were attracted to previously defoliated trees by some cues from the host plants, HIPVs being the most likely candidates. The third trophic level should thus be considered in natural plant herbivore interactions. Furthermore, parasitoids and food resources are key factors in the population regulation of forest insect pests, and indirect plant defences could be important in their interactions. Our research also emphasizes the quality of control treatments in field experiments, since immediate plant responses easily obscure the results as soon as control trees become infested by herbivorous insects.