Tendencies in the Herring Population Development of the Baltic Sea

During the 1960's a change in population structure of Baltic herring started which resulted in the dominance of spring spawners in the entire Baltic since the beginning 1970's. Autumn spawning herring is very rare in the yields of fisheries since. This development has been accompanied by a likely increase of the total stock biomass of herring in the area. Yields of herring fisheries increased remarkable up to 1984, partly as a result of increased fishing effort. Recent developments of stock biomasses point to dependencies on fluctuations of growth rates. Growth is influenced by several environmental factors but is very likely especially dependent on abundance of food and on temperature. Eutrophication of the Baltic Sea increased perhaps the abundance of food for the planktonfeeding herring but it may have been contributing to the depletion of autumn spawning herring via the declining oxygen content of bottom water layers during the past 20 years.     

Homozygosity Haplotype and Whole-Exome Sequencing Analysis to Identify Potentially Functional Rare Variants Involved in Multiple Sclerosis among Sardinian Families

Multiple Sclerosis (MS) is a complex multifactorial autoimmune disease, whose sex- and age-adjusted prevalence in Sardinia (Italy) is among the highest worldwide. To date, 233 loci were associated with MS and almost 20% of risk heritability is attributable to common genetic variants, but many low-frequency and rare variants remain to be discovered. Here, we aimed to contribute to the understanding of the genetic basis of MS by investigating potentially functional rare variants. To this end, we analyzed thirteen multiplex Sardinian families with Immunochip genotyping data. For five families, Whole Exome Sequencing (WES) data were also available. Firstly, we performed a non-parametric Homozygosity Haplotype analysis for identifying the Region from Common Ancestor (RCA). Then, on these potential disease-linked RCA, we searched for the presence of rare variants shared by the affected individuals by analyzing WES data. We found: (i) a variant (43181034 T > G) in the splicing region on exon 27 of CUL9; (ii) a variant (50245517 A > C) in the splicing region on exon 16 of ATP9A; (iii) a non-synonymous variant (43223539 A > C), on exon 9 of TTBK1; (iv) a non-synonymous variant (42976917 A > C) on exon 9 of PPP2R5D; and v) a variant (109859349-109859354) in 3′UTR of MYO16.     

Revisiting the notion of deleterious sweeps

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites—both in the presence and absence of interference amongst deleterious mutations—and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of F_ST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.     

The miR-302c/transforming growth factor-β receptor type-2 axis modulates interleukin-1β-induced degenerative changes in osteoarthritic chondrocytes

Chondrocyte production of catabolic and inflammatory mediators participating in extracellular matrix degradation has been regarded as a central event in osteoarthritis (OA) development. During OA pathogenesis, interleukin-1β (IL-1β) decreases the mRNA expression and protein levels of transforming growth factor-β receptor type-2 (TGFBR2), thus disrupting transforming growth factor-β signaling and promoting OA development. In the present study, we attempted to identify the differentially expressed genes in OA chondrocytes upon IL-1β treatment, investigate their specific roles in OA development, and reveal the underlying mechanism. As shown by online data analysis and experimental results, TGFBR2 expression was significantly downregulated in IL-1β-treated human primary OA chondrocytes. IL-1β treatment induced degenerative changes in OA chondrocytes, as manifested by increased matrix metalloproteinase 13 and a disintegrin and metalloproteinase with thrombospondin motifs 5 proteins, decreased Aggrecan and Collagen II proteins, and suppressed OA chondrocyte proliferation. These degenerative changes were significantly reversed by TGFBR2 overexpression. miR-302c expression was markedly induced by IL-1β treatment in OA chondrocytes. miR-302c suppressed the expression of TGFBR2 via direct binding to its 3′- untranslated region. Similar to TGFBR2 overexpression, miR-302c inhibition significantly improved IL-1β-induced degenerative changes in OA chondrocytes. Conversely, TGFBR2 silencing enhanced IL-1β-induced degenerative changes and significantly reversed the effects of miR-302c inhibition in response to IL-1β treatment. In conclusion, the miR-302c/TGFBR2 axis could modulate IL-1β-induced degenerative changes in OA chondrocytes and might become a novel target for OA treatment.Electronic supplementary materialThe online version of this article (10.1007/s12079-020-00591-2) contains supplementary material, which is available to authorized users.     

Tracing the Origin and Evolutionary Fate of Recent Gene Retrocopies in Natural Populations of the House Mouse

Although the contribution of retrogenes to the evolution of genes and genomes has long been recognized, the evolutionary patterns of very recently derived retrocopies that are still polymorphic within natural populations have not been much studied so far. We use here a set of 2,025 such retrocopies in nine house mouse populations from three subspecies (Mus musculus domesticus, M. m. musculus, and M. m. castaneus) to trace their origin and evolutionary fate. We find that ancient house-keeping genes are significantly more likely to generate retrocopies than younger genes and that the propensity to generate a retrocopy depends on its level of expression in the germline. Although most retrocopies are detrimental and quickly purged, we focus here on the subset that appears to be neutral or even adaptive. We show that retrocopies from X-chromosomal parental genes have a higher likelihood to reach elevated frequencies in the populations, confirming the notion of adaptive effects for “out-of-X” retrogenes. Also, retrocopies in intergenic regions are more likely to reach higher population frequencies than those in introns of genes, implying a more detrimental effect when they land within transcribed regions. For a small subset of retrocopies, we find signatures of positive selection, indicating they were involved in a recent adaptation process. We show that the population-specific distribution pattern of retrocopies is phylogenetically informative and can be used to infer population history with a better resolution than with SNP markers.     

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.     

Remarkably Low KIR and HLA Diversity in Amerindians Reveals Signatures of Strong Purifying Selection Shaping the Centromeric KIR Region

The killer-cell immunoglobulin-like receptors (KIR) recognize human leukocyte antigen (HLA) molecules to regulate the cytotoxic and inflammatory responses of natural killer cells. KIR genes are encoded by a rapidly evolving gene family on chromosome 19 and present an unusual variation of presence and absence of genes and high allelic diversity. Although many studies have associated KIR polymorphism with susceptibility to several diseases over the last decades, the high-resolution allele-level haplotypes have only recently started to be described in populations. Here, we use a highly innovative custom next-generation sequencing method that provides a state-of-art characterization of KIR and HLA diversity in 706 individuals from eight unique South American populations: five Amerindian populations from Brazil (three Guarani and two Kaingang); one Amerindian population from Paraguay (Aché); and two urban populations from Southern Brazil (European and Japanese descendants from Curitiba). For the first time, we describe complete high-resolution KIR haplotypes in South American populations, exploring copy number, linkage disequilibrium, and KIR–HLA interactions. We show that all Amerindians analyzed to date exhibit the lowest numbers of KIR–HLA interactions among all described worldwide populations, and that 83–97% of their KIR–HLA interactions rely on a few HLA-C molecules. Using multiple approaches, we found signatures of strong purifying selection on the KIR centromeric region, which codes for the strongest NK cell educator receptors, possibly driven by the limited HLA diversity in these populations. Our study expands the current knowledge of KIR genetic diversity in populations to understand KIR–HLA coevolution and its impact on human health and survival.     

Estimating Competition in Cladocerans Using Data on Dynamics of Clutch Size and Population Density

Negative correlations between clutch size and population density are proposed to be considered as indices of intra- and interspecific competition in cladocerans if they are revealed while analyzing population dynamics and clutch size and time lags are taken into account. The proper correlation analysis of summer populations of Diaphanosoma brachyurum, Bosmina coregoni, Daphnia cucullata and D. galeata from mesotrophic Lake Glubokoye (Moscow Region) in 1975, 1978, and 1979 indicates the important role of competition of both types for the community studied. High niche overlap in food and space in the four populations was also observed.     

Individual small in‐stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa

Water flow in river networks is frequently regulated by man‐made in‐stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in‐stream barriers exist worldwide, their impact on dispersal of macroinvertebrates remains unclear. Therefore, we, therefore, assessed the effects of such barriers on the population structure and effective dispersal of five macroinvertebrate species with strictly aquatic life cycles: the amphipod crustacean Gammarus fossarum (clade 11), three snail species of the Ancylus fluviatilis species complex and the flatworm Dugesia gonocephala. We studied populations at nine weirs and eight culverts (3 pipes, 5 tunnels), built 33–109 years ago, mainly in the heavily fragmented catchment of the river Ruhr (Sauerland, Germany). To assess fragmentation and barrier effects, we generated genome‐wide SNP data using ddRAD sequencing and evaluated clustering, differentiation between populations up‐ and downstream of each barrier and effective migration rates among sites and across barriers. Additionally, we applied population genomic simulations to assess expected differentiation patterns under different gene flow scenarios. Our data show that populations of all species are highly isolated at regional and local scales within few kilometers. While the regional population structure likely results from historical processes, the strong local differentiation suggests that contemporary dispersal barriers exist. However, we identified significant barrier effects only for pipes (for A. fluviatilis II and III) and few larger weirs (>1.3 m; for D. gonocephala). Therefore, our data suggest that most small in‐stream barriers can probably be overcome by all studied taxa frequently enough to prevent fragmentation. However, it remains to be tested if the strong local differentiation is a result of a cumulative effect of small barriers, or if larger in‐stream barriers, land use, chemical pollution, urbanization, or a combination of these factors impede gene flow.     

Reduced habitat quality increases intrinsic but not ecological costs of reproduction

Although the costs of reproduction are predicted to vary with the quality of the breeding habitat thereby affecting population dynamics and life‐history trade‐offs, empirical evidence for this pattern remains sparse and equivocal. Costs of reproduction can operate through immediate ecological mechanisms or through delayed intrinsic mechanisms. Ignoring these separate pathways might hinder the identification of costs and the understanding of their consequences. We experimentally investigated the survival costs of reproduction for adult little owls (Athene noctua) within a gradient of habitat quality. We supplemented food to nestlings, thereby relieving the parents’ effort for brood provisioning. We used radio‐tracking and Bayesian multistate modeling based on marked recapture and dead recovery to estimate survival rates of adult little owls across the year as a function of food supplementation and habitat characteristics. Food supplementation to nestlings during the breeding season increased parental survival not only during the breeding season but also during the rest of the year. Thus, the low survival of parents of unfed broods likely represents both, strong ecological and strong intrinsic costs of reproduction. However, while immediate ecological costs occurred also in high‐quality habitats, intrinsic costs carrying over to the post‐breeding period occurred only in low‐quality habitats. Our results suggest that immediate costs resulting from ecological mechanisms such as predation, are high also in territories of high habitat quality. Long‐term costs resulting from intrinsic trade‐offs, however, are only paid in low‐quality habitats. Consequently, differential effects of habitat quality on immediate ecological and delayed intrinsic mechanisms can mask the increase of costs of reproduction in low‐quality breeding habitats. Intrinsic costs may represent an underrated mechanism of habitat quality affecting adult survival rate thereby considerably accelerating population decline in degrading habitats. This study therefore highlights the need for a long‐term perspective to fully assess the costs of reproduction and the role of habitat quality in modifying these costs.