Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.

The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic counting methods and the maximum-likelihood (ML) method based on a codon substitution model are widely used for such analysis. However, these methods do not have nice statistical properties, as the estimates can be zero or infinity in some data sets, so that their means and variances are infinite. In large genome-scale comparisons, such extreme estimates (either 0 or ∞) of ω and sequence distance (t) are common. Here, we implement a Bayesian method to estimate ω and t in pairwise sequence comparisons. Using a combination of computer simulation and real data analysis, we show that the Bayesian estimates have better statistical properties than the ML estimates, because the prior on ω and t shrinks the posterior of those parameters away from extreme values. We also calculate the posterior probability for ω > 1 as a Bayesian alternative to the likelihood ratio test. The new method is computationally efficient and may be useful for genome-scale comparisons of protein-coding gene sequences

The last hideout: Abundance patterns of the not-quite-yet extinct mayfly Prosopistoma pennigerum in the Albanian Vjosa River network

1. The mayfly Prosopistoma pennigerum (Müller, 1785) (Insecta: Ephemeroptera) once occurred in many European river networks. However, observations decreased in the last decades and the species can be considered largely extinct throughout Europe due to river alterations. 2. Only three extant populations are known from Cabriel (southern Spain), Volga (Russia) and Vjosa (Albania) rivers. 3. We recorded the species along a 150 km stretch in the Vjosa River in three sampling seasons (spring 2018, fall 2018 and fall 2019), counting up to 302 P. pennigerum per m2, the highest recorded abundance for the species to date. Moreover, we detected traces of environmental DNA in a newly designed targeted eDNA assay. 4. In our modelling approach we define the species’ niche in a theoretically available niche space given by the Vjosa River network and predict a high probability of presence (θ) in downstream located sections of this river. Expected abundances (λ) could be related to a set of environmental variables, importantly to higher discharge and increased sediment dynamics. 5. Simultaneous occurrence of larvae of different sizes at individual sites suggests an asynchronous life cycle, which may be advantageous to cope with the highly dynamic river hydrology. 6. The P. pennigerum population in the Vjosa is of key importance for the species’ global survival

Neutral variation does not predict immunogenetic variation in the European grayling (Thymallus thymallus) - implications for management

Preservation of genetic diversity is critical to successful conservation and there is increasing demand for the inclusion of ecologically meaningful genetic information in management decisions. Supportive breeding programmes are increasingly implemented to combat declines in many species, yet their effect on adaptive genetic variation is understudied. This is despite the fact that supportive breeding may interfere with natural evolutionary processes. Here, we assessed the performance of neutral and adaptive markers (Major Histocompatibility Complex; MHC) to inform management of European grayling (Thymallus thymallus), which routinely involves supplementation of natural populations with hatchery‐reared fish (stocking). This study is the first to characterize MH II DAA and DAB loci in grayling and to investigate immune genetic variation in relation to management practice in this species. High‐throughput Illumina sequencing of ‘introduced’, ‘stocked native’ and ‘non‐stocked native’ populations revealed significantly higher levels of allelic richness and heterozygosity for MH markers than microsatellites exclusively in non‐stocked native populations. Likewise, significantly lower differentiation at the MH II than for microsatellites was apparent when considering non‐stocked native populations, but not stocked populations. We developed a simulation model to test the effects of relaxation of selection during the early life stage within captivity. Dependent on the census population size and stocking intensity, there may be long‐term effects of stocking on MH II, but not neutral genetic diversity. This is consistent with our empirical results. This study highlights the necessity for considering adaptive genetic variation in conservation decisions and raises concerns about the efficiency of stocking as a management practice

Natural Selection and Genetic Drift: Neutral and adaptive genetic variability of hatchery versus wild populations in brown trout Salmo trutta

Genetic drift and natural selection are two of the major forces shaping the genetic makeup of a population. Genetic drift reduces genetic variability due to the random loss of alleles during the transition from one generation to the next one. The smaller the population, the stronger genetic drift is. Natural selection favors the spread of specific alleles within a population over time, namely those alleles that are beneficial in the specific environment of this population. Individuals that carry alleles that are less advantageous have a lower probability to survive and reproduce. For establishing a captive population, very often, only a small number of individuals are taken and the number breeding individuals used to maintain the population is limited, thus increasing the amount of genetic drift. On the other hand, the drastically different environment in captivity (artificial diet, higher individual density, altered pathogen pressure, etc.) may favor alleles that are maladaptive for individuals when they are released back in the wild, e.g. for stocking measures. We screened both, neutral and adaptive genetic markers, in order to assess the relative importance of genetic drift and selection pressure on wild and hatchery populations of Austrian brown trout. We confirm a strong positive selection pressure on an adaptive locus of the Major histocompatibility Complex (MHC), whereas the signal of this selection pressure was more pronounced in hatchery populations. This may either stem from stronger genetic drift in wild populations due to smaller effective population sizes or a stronger directional selection in these wild populations, whereby only particular genetic variants proved to be adaptive in each specific environment. Therefore, the alleles arising from the hatchery selection regime may be detrimental in the wild, which can lead to lower survival rates of stocked fish in wild environments

Isolation and characterization of the CYP2D6 gene in Felidae with comparison to other Mammals

Cytochrome P450 (auch CYPs oder P450s) stellen eine Superfamilie an Hämproteinen dar und sind vor allem dadurch bekannt, dass sie am Metabolismus von etwa 75% der humanmedizinischen Medikamente am Markt beteiligt sind. Weiters spielen eine wichtige Rolle in der Biosynthese von Steroidhormonen, der Oxidation von ungesättigten Fettsäuren und dem Metabolismus von fettlöslichen Proteinen und werden auch mit der Aktivierung von Prokarzinogenen in Verbindung gebracht. Verschiedene Allelvarianten mehrerer P450 Gene verursachen eine hohe Variabilität in Abbau- und Ausscheidungsgeschwindigkeit von bestimmten Medikamenten zwischen einzelnen Personen. Das hochvariable CYP2D6-Gen ist das wohl am besten untersuchte Mitglied der P450 Gen-Superfamilie und CYP2D6 ist am Abbau von etwa 25% der handelsüblichen Medikamente beteiligt. Im Gegensatz zu den zahlreichen detaillierten Studien in Menschen ist noch sehr wenig über mögliche Variabilität in Sequenz und Funktion dieses Gens in Tieren bekannt. Orthologe des CYP2D6-Gens wurden in mehreren Tieren von veterinärmedizinischem Interesse charakterisiert, wobei das Hauptinteresse der P450-Forschung in Tieren in der Expression und Substratspezifität des Enzyms liegt.CYP2D6-mRNA von 23 Vertretern der Familie Felidae, sieben Arten umfassend, wurde sequenziert und mit bereits zur Verfügung stehenden Sequenzen zehn weiterer Säugetierarten und mehreren Allelvarianten des Menschen verglichen.Ein relativ hohes dN/dS-Verhältnis zwischen den Sequenzen wurde beobachtet, vor allem innerhalb der Katzenfamilie. Eine nicht-monotone Verteilung der paarweisen dN/dS-Verhältnisse in Abhängigkeit zur evolutionären Distanz weist auf den Erhalt von leicht schädlichen Mutationen im Zeitraum von drei bis vier Millionen Jahren hin. Weiters wurden Hinweise positiver Selektion auf einzelne Codons gefunden und ein möglicher Zusammenhang zwischen dem Ernährungstyp einzelner Arten und der Aminosäurezusammensetzung an Substratbindestellen wird diskutiert.Cytochrome P450s (CYPs, P450s) are a superfamily of hemoproteins best known by the fact that they metabolize about 75% of marketed human drugs. P450s additionally play important roles in the biosynthesis of steroid hormones, oxidation of unsaturated fatty acids and the metabolism of fat-soluble proteins and are also involved in the activation of procarcinogens. Allelic variants of several human P450 genes underlie the high among individual variation in metabolic conversion and excretion rates of drugs and therefore drug response. The highly polymorphic CYP2D6 gene is the best studied member of the P450 gene superfamily, accounting for about 25% of the metabolism of commonly used drugs. In contrast to detailed studies of this enzyme and its gene in humans, little is known about the sequence variation or function of this gene in non-human animals. Orthologs of the CYP2D6 gene have been characterized in several animals of interest to veterinary medicine, whereby the main focus of P450 research in animals is expression and substrate specificity.CYP2D6-mRNA from 23 cats (Felidae) spanning seven species were sequenced and compared to available CYPD6-sequences in ten additional mammals including multiple allelic variants in humans.A relatively high mean dN/dS ratio among the sequences is revealed, especially within Felidae. A non-monotonic distribution in pairwise dN/dS ratios with respect to evolutionary distance suggests the retention of slightly deleterious mutations across three to four MY. Signals of positive selection pressure on specific codons are supported and the possible connection between the dietary type of specific species and specific amino acid changes in substrate binding sites is discussed.Tamara SchenekarZsfassung in dt. SpracheGraz, Univ., Masterarb., 2010(VLID)21345

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Biodiversity monitoring via environmental DNA, particularly metabarcoding, isevolving into a powerful assessment tool for riverine systems. However, formetabarcoding to be fully integrated into standardized monitoring programmes, somecurrent challenges concerning sampling design, laboratory workflow, and data analy-sis need to be overcome. Here, we review some of these major challenges and poten-tial solutions. We further illustrate three potential pitfalls, namely the choice ofsuitable metabarcoding primers, the necessity of complete reference databases, andvarying assay sensitivities, by a reappraisal of our-own recently carried outmetabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish(Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, inthe same samples. Furthermore, after extending the genetic reference database by12 additional species and re-analysing the metabarcoding data, we additionallydetected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey(Eudontomyzon mariae) and reassigned the operational taxonomic units previouslyassigned toMisgurnus fossilistoCobitis sibirica. In silico analysis of metabarcodingprimer efficiencies revealed considerable variability among primer pairs and amongtarget species, which could lead to strong primer bias and potential false-negatives inmetabarcoding studies if not properly compensated for. These results highlight someof the pitfalls of eDNA-metabarcoding as a means of monitoring fish biodiversity inlarge rivers, which need to be considered in order to fully unleash the full potential ofthese approaches for freshwater biodiversity monitori

Genetic integrity of European grayling (Thymallus thymallus L. 1758) population within the Vienne River drainage basin after five decades of stockings

International audienc

Evaluating a species phylogeny using ddRAD SNPs: cytonuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae)

International audienceHybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for all Thymallus (Salmonidae) species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species. The newly obtained nuclear phylogeny was largely concordant with a previously published mitogenome-based topology but revealed a few cyto-nuclear discordances. These incongruencies primarily involved the placement of internal nodes rather than the resolution of species, except for one European species where anthropogenic stock transfers are thought to be responsible for the observed pattern. The analysis of four contact zones where multiple species are found revealed a few cases of mitochondrial capture and limited signals of nuclear introgression. Interestingly, the mechanisms restricting interspecific gene flow might be distinct; while in zones of secondary contact, small-scale physical habitat separation appeared as a limiting factor, biologically based reinforcement mechanisms are presumed to be operative in areas where species presumably evolved in sympatry. Signals of historical introgression were largely congruent with the routes of species dispersal previously inferred from mitogenome data. Overall, the ddRADseq dataset provided a robust phylogenetic reconstruction of the genus Thymallus including new insights into historical hybridization and introgression, opening up new questions concerning their evolutionary history