Development and application of a second-generation multilingual tool for invasion risk screening of non-native terrestrial plants.

Under the increasing threat to native ecosystems posed by non-native species invasions, there is an urgent need for decision support tools that can more effectively identify non-native species likely to become invasive. As part of the screening (first step) component in non-native species risk analysis, decision support tools have been developed for aquatic and terrestrial organisms. Amongst these tools is the Weed Risk Assessment (WRA) for screening non-native plants. The WRA has provided the foundations for developing the first-generation WRA-type Invasiveness Screening Kit (ISK) tools applicable to a range of aquatic species, and more recently for the second-generation ISK tools applicable to all aquatic organisms (including plants) and terrestrial animals. Given the most extensive usage of the latter toolkits, this study describes the development and application of the Terrestrial Plant Species Invasiveness Screening Kit (TPS-ISK). As a second-generation ISK tool, the TPS-ISK is a multilingual turnkey application that provides several advantages relative to the WRA: (i) compliance with the minimum standards against which a protocol should be evaluated for invasion process and management approaches; (ii) enhanced questionnaire comprehensiveness including a climate change component; (iii) provision of a level of confidence; (iv) error-free computation of risk scores; (v) multilingual support; (vi) possibility for across-study comparisons of screening outcomes; (vii) a powerful graphical user interface; (viii) seamless software deployment and accessibility with improved data exchange. The TPS-ISK successfully risk-ranked five representative sample species for the main taxonomic groups supported by the tool and ten angiosperms previously screened with the WRA for Turkey. The almost 20-year continuous development and evolution of the ISK tools, as opposed to the WRA, closely meet the increasing demand by scientists and decision-makers for a reliable, comprehensive, updatable and easily deployable decision support tool. For terrestrial plant screening, these requirements are therefore met by the newly developed TPS-ISK.

Effect of Microplastics on the Activity of Digestive and Oxidative-Stress-Related Enzymes in Peled Whitefish (Coregonus peled Gmelin) Larvae.

Microplastics (MPs) are emergent pollutants in freshwater environments and may impact aquatic organisms, including those of nutritional value. The specific activities of digestive and antioxidant enzymes can be used as good bioindicators of the potential effects of MPs on fish in case of waterborne MP contamination. In this study, we used fluorescent polystyrene microplastics (PS-MPs) to analyze the alterations in enzyme activities in larvae of Coregonus peled Gmelin (peled or Northern whitefish), one of the most valuable commercial fish species of Siberia. Our results indicate that peled larvae can ingest 2 µm PS microspheres in a waterborne exposure model. A positive correlation (rs = 0.956; p < 0.01) was found between MP concentration in water and the number of PS microspheres in fish guts, with no significant differences between 24 h and 6-day exposure groups. The ingestion of MPs caused alterations in digestive enzyme activity and antioxidant responses at the whole-body level. The presence of PS-MPs significantly stimulated (p < 0.05) the specific activity of α-Amylase and non-specific esterases in peled larvae after 24 h. However, a pronounced positive effect (p < 0.05) of MPs on the activity of pancreatic trypsine and bile salt-activated lipase was only found after 6 days of exposure compared to after 24 h. Intestinal membrane enzyme aminopeptidase N was also stimulated in the presence of PS-MPs after 6-day exposure. We also observed a significant increase in the specific activity of catalase in peled larvae after 6 days of exposure, which indicates the MP-induced modulation of oxidative stress. Taken together, these results highlight the potential impact of environmental MPs on northern commercial fish, their importance for estimating fish stocks, and the sustainability of freshwater ecosystems.

Freshwater and brackish water fishes of Sakhalin Island (Russia) in inland and coastal waters: an annotated checklist with taxonomic comments.

Based on a critical analysis of scientific publications for the last 200 years and on the collected specimens, a complete annotated list of both typical freshwater ichthyofauna of Sakhalin Island, with the inclusion of marine species that can be found in brackish coastal waters, is reported for the first time. The annotated list includes 226 species classified in three classes, 26 orders, 68 families, 29 subfamilies, and 148 genera. For 160 species, information is provided on collection samples deposited in various museums around the world, 36 of which are type specimens. For each species, conservation status (according to IUCN Red List of Threatened Species and the Red Book of the Sakhalin region), zoogeographic characteristics (distribution within Sakhalin Island and globally), abundance and commercial value are given. For a number of species, more detailed information on synonymy and nomenclature is provided. The study area is located in the western North Pacific and includes the entire coast of Sakhalin Island in the Sea of Okhotsk and the northern Sea of Japan, as well as the adjacent Sea of Okhotsk coast of northern Hokkaido, Japan.

Impacts of environmental change on biodiversity and vegetation dynamics in Siberia.

Biological diversity is the basis for, and an indicator of biosphere integrity. Together with climate change, its loss is one of the two most important planetary boundaries. A halt in biodiversity loss is one of the UN Sustainable Development Goals. Current changes in biodiversity in the vast landmass of Siberia are at an initial stage of inventory, even though the Siberian environment is experiencing rapid climate change, weather extremes and transformation of land use and management. Biodiversity changes affect traditional land use by Indigenous People and multiple ecosystem services with implications for local and national economies. Here we review and analyse a large number of scientific publications, which are little known outside Russia, and we provide insights into Siberian biodiversity issues for the wider international research community. Case studies are presented on biodiversity changes for insect pests, fish, amphibians and reptiles, birds, mammals and steppe vegetation, and we discuss their causes and consequences.

Evolution of Tandemly Arranged Repetitive DNAs in Three Species of Cyprinoidei with Different Ploidy Levels.

Polyploid species represent a challenge for both cytogenetic and genomic studies due to their high chromosome numbers and the morphological similarity between their paralogous chromosomes. This paper describes the use of low-coverage high-throughput sequencing to identify the 14 most abundant tandemly arranged repetitive elements in the paleotetraploid genome of the crucian carp (Carassius carassius, 2n = 100). These repetitive elements were then used for molecular cytogenetic studies of a closely related functionally triploid form of the Prussian carp (Carassius gibelio, 3n = 150 + Bs) and a relatively distant diploid species, the tench (Tinca tinca, 2n = 48). According to their distribution on the chromosomes of the 3 aforementioned species, the repetitive elements here identified can be divided into 5 groups: (1) those specific to a single genomic locus in both Carassius species, despite the recent carp-specific genome duplication; (2) those located in a single genomic locus of T. tinca, but amplified in one or both Carassius species; (3) those massively amplified in the B chromosomes of C. gibelio; (4) those located in a single locus in C. gibelio, but amplified in many blocks in C. carassius; and (5) those located in multiple pericentromeric loci in both Carassius species. Our data indicate that some of the repetitive elements are highly conserved in cyprinoid species and may serve as good cytogenetic and genomic markers for discriminating paralogous chromosomes, while others are evolutionarily recent, and their amplification may be related to the last whole-genome duplication event.

The rise and fall of the ancient northern pike master sex-determining gene.

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii).

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.

Population genetic structure and phylogeography of sterlet (Acipenser ruthenus, Acipenseridae) in the Ob and Yenisei river basins.

The sterlet (Acipenser ruthenus Linnaeus, 1758) is a relatively small sturgeon widely distributed in Eurasian rivers from the Danube to the Yenisei. During the twentieth century, all wild sterlet populations have declined due to anthropogenic factors including: overfishing, poaching, construction of dams, and pollution. Despite the necessity of characterization both wild and captive stocks, few studies of population genetics have been performed thus far. Here we studied the genetic diversity and geographic structure of sterlet populations across the eastern range - Ob-Irtysh and Yenisei basins - by sequencing a 628-bp fragment of mitochondrial DNA control region. We identified 98 new haplotypes, delineated 12 haplogroups and estimated the time of basal haplogroup divergence within the species as over 8 million years ago. Our data suggest that Ob-Irtysh and Yenisei populations are isolated from each other and much lower genetic diversity is present in the Yenisei population than in the Ob-Irtysh population. Our data imply that sterlet populations in Siberian rivers underwent bottleneck or fragmentation, followed by subsequent population expansion. The data obtained here are important for sterlet population monitoring and restocking management.

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting.

BACKGROUND: Acipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied. RESULTS: Cell lines from different tissues of 12 sterlet specimens from Siberian populations were established following an optimized protocol. Conventional cytogenetic studies supplemented with molecular cytogenetic investigations on obtained fibroblast cell lines allowed a detailed description of sterlet karyotype and a precise localization of 18S/28S and 5S ribosomal clusters. Localization of sturgeon specific HindIII repetitive elements revealed an increased concentration in the pericentromeric region of the acrocentric ARUT14, while the total sterlet repetitive DNA fraction (C0t30) produced bright signals on subtelomeric segments of small chromosomal elements. Chromosome and region specific probes ARUT1p, 5, 6, 7, 8 as well as 14 anonymous small sized chromosomes (probes A-N) generated by microdissection were applied in chromosome painting experiments. According to hybridization patterns all painting probes were classified into two major groups: the first group (ARUT5, 6, 8 as well as microchromosome specific probes C, E, F, G, H, and I) painted only a single region each on sterlet metaphases, while probes of the second group (ARUT1p, 7 as well as microchromosome derived probes A, B, D, J, K, M, and N) marked two genomic segments each on different chromosomes. Similar results were obtained on male and female metaphases. CONCLUSIONS: The sterlet genome represents a complex mosaic structure and consists of diploid and tetraploid chromosome segments. This may be regarded as a transition stage from paleotetraploid (functional diploid) to diploid genome condition. Molecular cytogenetic and genomic studies of other 120- and 240-chromosomal sturgeons are needed to reconstruct genome evolution of this vertebrate group.