Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761.

The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction.

Assessment of Eurasian lynx reintroduction success and mortality risk in north-west Poland.

Despite recent local reintroductions of the Eurasian lynx Lynx lynx in central and north-eastern Poland, the increase in its population was not followed by its westward expansion. To address this problem and restore the lynx population in north-western Poland, 61 captive-born individuals of Baltic population origin were released in the province of Western Pomerania in 2019-2021. Prior to their release, all the animals underwent an adaptation training phase. They were then set free according to a hard-release protocol and subsequently monitored by means of GPS telemetry. In order to assess the short-term reintroduction success, the survival and causes of death of the released individuals were studied as a function of sex, age, training time, and release time and place. The overall survival rate was 71.15%, the median survival time 202 days. Most mortality, due to environmental factors, i.e. scabies (> 200 days) or traffic collisions (< 200 days), was recorded during the first 300 days following release. Age, year of release and training time were significantly related to survival, indicating that the older the lynx was when released, the better its survival changes. In contrast, the longer the training time, the poorer were the chances of survival. There was no evidence of any effect of sex, month of release or place of release. Based on these results, recommendations were made for the planning of further releases and measures to manage the restored population.

A Meta-Analytical Investigation of the Gap between Measured and Predicted Inter-Population Genetic Diversity in Species of High Conservation Concern-The Case of the Critically Endangered European Mink Mustela lutreola L., 1761.

Although properly designed sampling in population genetic studies is of key importance for planning evidence-informed conservation measures, sampling strategies are rarely discussed. This is the case for the European mink Mustela lutreola, a critically endangered species. In order to address this problem, a meta-analysis aiming to examine the completeness of mtDNA haplotype sampling in recent studies of M. lutreola inter-population genetic diversity was conducted. The analysis was performed using the sample-size-based rarefaction and extrapolation sampling curve method for three populations-the Northeastern (Russia, Belarus and Estonia), the Western (France and Spain), and the Southeastern (Romania). The extrapolated values of the Shannon-Wiener index were determined, assuming full sample coverage. The gap between the measured and predicted inter-population genetic diversity was estimated, indicating that the identified level of sample coverage was the lowest for the NE population (87%), followed by the SE population (96%) and the W population (99%). A guide for sampling design and accounting for sampling uncertainty in future population genetic studies on European mink is provided. The relatively low sample coverage for the Russian population clearly indicates an urgent need to take conservation measures for European mink in this country.

Assessment of Aleutian mink disease virus (AMDV) prevalence in feral American mink in Iceland. Case study of a pending epizootiological concern in Europe.

BACKGROUND: Recurring escapes or deliberate releases and subsequent infiltration or establishment of feral populations by individuals from fur farms have been commonly noted since the beginning of fur industry expansion. Once animals have invaded ecosystems adjacent to source farms escapees can change the demography of the feral populations through hybridization, outbreeding depression, competition and spreading of various pathogens which can decimate wild populations. In our study, we aimed to assess spread of Aleutian mink disease virus (AMDV) in the feral population of American mink (Neovison vison) in Iceland. The additional objective was to elucidate whether basic morpho-anatomical parameters (i.e., Fulton's condition factor or spleen to body weight ratio) might be used as a preliminary indicator of AMDV infection. METHODS: American mink (n = 164) were captured by professional hunters in 8 regions of Iceland. The detection of AMDV in the spleen of male and female individuals was based on PCR amplification of an NS1 gene fragment. RESULTS: We confirmed AMDV presence in 23.8% (n = 39) of collected samples with no significant difference in infection rate between males and females. Additionally, we revealed that the prevalence of virus in the feral population was higher closer to fur farms. However, the countrywide prevalence and direction of AMDV distribution needs to be further investigated. Comparison of condition indices in non-infected and infected animals showed significant deterioration of body and spleen parameters in the latter group. Therefore, the application of basic measurements of the American mink may be used to evaluate the health status of individuals in terms of pathogen infection. CONCLUSIONS: The study shed a new light on prevalence and distribution of AMDV in the feral population of American mink in Iceland and the results might be successfully applied to develop models to infer dynamics of various pathogens, even those latently transmitted by disease-free animals.

The effects of parental age difference on the offspring sex and fitness of European blackbirds.

BACKGROUND: Many studies of birds have indicated that offspring sex ratios can vary with environmental and parental traits. On the basis of long-term research, we first evaluated the possible influence of parental age difference and brood characteristics on offspring sex and fitness in multi-brooded Blackbirds Turdus merula. METHODOLOGY: The study was conducted in the city-centre Stefan Zeromski Park in Szczecin, NW Poland, where the local population of Blackbirds has been studied since 1996. Data on the offspring sex and fitness were collected in five years, 2005-2007 and 2016-2017. During the breeding season we inspected the study area to locate the pairs' territories and to track their nests and clutches. RESULTS: We found that the overall sex ratio did not differ statistically from 50:50, but that younger females bonded with older mates did tend to produce more sons, probably because of the greater fitness of male descendants. Accordingly, the sons' breeding success increased with the father's age, but this relationship was close to non-linear, which may indicate that the transgenerational effect of paternal senescence could negatively affect progeny fitness despite the high-quality of older fathers. Older females mated with younger males produced more daughters, which could have been due to the lesser attractiveness of the males and the mothers' poorer condition caused by accelerated senescence. We found that neither offspring hatching sequence nor hatching date or clutch sequence were significant for sex determination. CONCLUSIONS: We consider that in our Blackbird population, parental age could make a more significant contribution to shaping offspring sex and reproductive success.

Validation of Real-time PCR Reference Genes of Muscle Metabolism in Harvested Spiny-Cheek Crayfish (Faxonius limosus) Exposed to Seasonal Variation.

Real-time quantitative reverse transcription PCR (RT-qPCR) is a sensitive and broadly used technique of assessing gene activity. To obtain a reliable result, stably expressed reference genes are essential for normalization of transcripts in various samples. To our knowledge, this is the first systematic analysis of reference genes for normalization of RT-qPCR data in spiny-cheek crayfish (Faxonius limosus). In this study, expression of five candidate reference genes (actb, ß-actin; gapdh, glyceraldehyde-3-phosphate dehydrogenase; eif, eukaryotic translation initiation factor 5a; ef-1α, elongation factor-1α; and tub, α-tubulin) in muscle samples from male and female F. limosus in spring and autumn was analyzed. Additionally, the most stable reference genes were used for accurate normalization of five target genes, i.e., tnnc, troponin c; ak, arginine kinase; fr, ferritin; ccbp-23, crustacean calcium-binding protein 23; and actinsk8, skeletal muscle actin 8. Results obtained using the geNorm and NormFinder algorithms showed high consistency, and differences in the activity of the selected actb with eif genes were successfully identified. The spring and autumn activities of the target genes (except ak) in the muscle tissue of males and females differed significantly, showing that both sexes are immensely involved in an array of breeding behaviors in spring, and females intensively recover in the autumn season. Characterization of first reference genes in spiny-cheek crayfish will facilitate more accurate and reliable expression studies in this key species.

GEOGRAPHIC AND ECOLOGIC ASPECTS OF THE COMMUNITY STRUCTURE OF TREMATODES OF MALLARDS (ANAS PLATYRHYNCHOS) IN NORTHERN POLAND AND THE CZECH REPUBLIC.

Trematode infestation of Mallards (Anas platyrhynchos) varies between northern Poland and the Czech Republic. We determined the trematode fauna of juvenile and adult Mallards from Poland in 2010-16 (n=79 Mallards) and from the Czech Republic in 1964-2001 (n=296). Infracommunity diversity of trematodes from juvenile Mallards, defined by the Brillouin index and mean number of species, was significantly greater in Poland than it was in the Czech Republic. There were more species and greater biodiversity in the trematode communities of Mallards from Poland, where the environment is more natural and less altered by human activity than it is in the Czech Republic. In the trematode community of juvenile Mallards, the Simpson's index of biodiversity was higher in the Czech Republic than it was in Poland. The Berger-Parker dominance index was comparable in both countries. In terms of prevalence, the structure of the trematode fauna was hierarchic, and trematode species had different positions in this hierarchy in the two countries. Statistically significant differences in the epidemiologic indices between infection of juvenile Mallards from Poland and the Czech Republic were noted for Bilharziella polonica, Echinostoma miyagawai, Echinostoma revolutum, Prosthogonimus cuneatus, Prosthogonimus ovatus, Notocotylus attenuatus, Echinoparyphium recurvatum, Australapatemon minor, Apatemon gracilis, Cyathocotyle prussica, Hypoderaeum conoideum, Metorchis xanthosomus, Psilochasmus oxyurus, and Cotylurus cornutus.

Spiny-Cheek Crayfish, Faxonius limosus (Rafinesque, 1817), as an Alternative Food Source.

The aim of the study was to present a comprehensive characterisation of crayfish meat, which is crucial to assess its potential usefulness in the food industry. To this end, we assessed the yield, basic chemical composition (protein, fat, minerals), nutritional value (amino acid and fatty acid profiles, essential amino acid index (EAAI), chemical score of essential amino acids (CS), hypocholesterolaemic/hypercholesterolaemic ratio (h/H), atherogenicity (AI) and thrombogenicity (TI) indices), as well as culinary value (lab colour, texture, sensory characteristics, structure) of the meat of spiny-cheek crayfish (Faxonius limosus) (n = 226) from Lake Sominko (Poland) harvested in May-September 2017. Crayfish meat, especially that from the abdomen, was shown to have high nutritional parameters. It is lean (0.26% of fat), with a favourable fatty acid profile and a very high quality of fat (PUFA (sum of polyunsaturated fatty acids):SFA (sum of saturated fatty acids), n-6/n-3, h/H, AI, TI) and protein (high CS and EAAI). It is also a better source of Ca, K, Mg, Na, P, and Cu than meat from slaughter animals. Hence, crayfish meat can be an alternative to livestock meat in the human diet. Owing to its culinary value (delicateness, weak game flavour, and odour), it meets the requirements of the most demanding consumers, i.e., children and older people.

Genetic diversity in natural populations of noble crayfish (Astacus astacus L.) in north-western Poland on the basis of combined SSR and AFLP data.

BACKGROUND: Conservation of noble crayfish (Astacus astacus) populations is becoming particularly important since the number of individuals is rapidly declining across the distribution range of the species in Europe. Five crayfish populations in northwestern Poland have been constantly monitored for two decades. However, the genetic structure of these populations has not been analysed, although this information is important to devise effective conservation strategies. METHODS: Noble crayfish were collected in the autumn of 2014 by scuba diving in Lakes Graniczne, Babinki, Biwakowe, Seki and Kwisno, all of which are situated in the Bytów Lakeland of northwestern Poland. Genetic diversity of the five populations was assessed based on allele variability in nine SSR regions and six AFLP primer combinations. RESULTS: Microsatellite results analysed with AMOVA showed that the diversity between populations corresponds to 18% of total variability, which was confirmed by similar results obtained using AFLP. Additionally, significant genetic diversity was revealed by high average FST values. All of the studied crayfish populations significantly deviated from the expected Hardy-Weinberg genetic equilibrium and were characterised by negative values of inbreeding coefficient (FIS). DISCUSSION: The invariably negative inbreeding coefficients (FIS) suggest a low number of mating individuals, a possible consequence of the phenomenon known as genetic bottleneck. However, additional comprehensive analyses are needed to assess the genetic structure, origin and vulnerability of the remaining populations of noble crayfish in the Bytów Lakeland of northwestern Poland, which have high conservation value and are particularly important as a live genetic bank for breeding and restitution purposes.

Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers.

BACKGROUND: Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. METHODS: The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA). RESULTS: The low value of Dice's coefficient (0.369) along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. DISCUSSION: The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.

A comparative study on the parasite fauna of perch, Perca fluviatilis L., collected from a freshwater coastal lake, brackish-water Baltic Sea, and the interconnecting canal.

BACKGROUND: Parasitological surveys of freshwater fishes rarely include comparisons between two ecologically different bodies of water. Such studies might help to understand processes of establishment of parasite faunas in estuary areas. The results obtained could also provide useful tools for discriminating various fish populations based on the composition of their parasite faunas. The present authors attempted to study such data from Resko Lake-a freshwater coastal lagoon (6 km2 surface area), and the adjacent areas of the Baltic Sea. Resko Lake, located 12 km west of the city of Kolobrzeg, is shallow (1.5 m) and is connected to the sea through a small canal (1.3 km long, 30 m wide). MATERIAL AND METHODS: The material was collected from April 1969 and July 1970. A total of 159 perch were collected, in this number 104 fish from the lake, 43 from the sea, and 12 from the canal. RESULTS: A total of 32 parasite species were recovered from the fish necropsied. The parasites represented 7 higher taxa: Protozoa (3 species), Cestoda (4), Digenea (13), Nematoda (5), Acanthocephala (3), Mollusca (1), and Crustacea (3). The parasite fauna of perch from the sea was definitely more abundant (31 species) compared to that of the lake (21), and the canal (12 species). Infection parameters of 13 parasite species demonstrated significant differences between the locations studied. The infection level of 6 parasite species was significantly higher in perch from the sea: Bothriocephalus scorpii, Ligula sp., Brachyphallus crenatus, Camallanus truncatus, Hysterothylacium aduncum, and Echinorhynchus gadi. On the other hand, infection levels of 7 other species were higher at the lake: Triaenophorus nodulosus, Bucephalus polymorphus, Azygia lucii, Tylodelphys clavata, Camallanus lacustris, Acanthocephalus lucii, and Achtheres percarum. The infection parameters of the fish from canal were similar to those from the lake. Interesting observations were made on the seasonality of certain parasites of both lake- and Baltic perch. The presently observed differences between parasite faunas of the fish from ecologically different adjacent estuarine locations are certainly caused by diversified environmental conditions that affected the processes of formation of the parasite communities there. Among important factors that could affect compositions of the parasite faunas could have been: availability of the intermediate hosts, exchange of waters (Baltic water influxes to the lake), fish migrations (spawning), and finally the separate identity of the two fish stocks studied.