Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.info:eu-repo/semantics/publishedVersio

First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity

Understanding how environmental and ecological factors shape variability in soil-associated microbial communities is a complex problem, particularly on islands, which contain a wide range of diverse and unique geology, fauna, and flora. The island of Crete features sharp altitudinal gradients, diverse landscapes, and distinct ecological zones shaped by its complex geological history making it an ideal natural laboratory for studying how environmental variation influences soil microbial communities. In this study, we characterized the soil microbial communities across Crete's ecozones and identify environmental factors associated with their diversity and composition. We performed a single-day, island-wide soil microbiota investigation, the first of its kind, to address this challenge by eliminating sources of variability including seasonality, weather conditions, anthropogenic or land use changes over time, and ecological succession of microbial communities. This island collection event (Island Sampling Day, ISD) was conducted in conjunction with the annual meeting of the Genomic Standards Consortium, on the island of Crete, and utilized standard data and metadata collection protocols. We generated amplicon sequences (V3-V4 regions of the 16 S ribosomal RNA gene) and a metadata-enriched dataset from 435 soil samples across 72 sites and four distinct ecozones for future whole-island microbiome studies. Here we report on the study design and sample collection process along with our initial examination of the ecological drivers of soil microbial community variability (e.g., elevation, soil types, soil pH, soil moisture, vegetation type, land use) across the Crete ecozones (defined by elevation and distinct habitats)

Estimating dung decay rates of roe deer (Capreolus capreolus) in different habitat types of a Mediterranean ecosystem: An information theory approach

For elusive species living in concealing habitats (e.g. deer in a forest habitat), indirect methods such as faecal pellet counts are considered more practical means of estimating population density and abundance. Accurate estimation of deer density using the faecal standing crop (FSC) method necessitates the reliable estimation of the mean time to decay of pellet groups present during the survey. Mean time to decay is generally habitat specific, and separate estimations should be made for each habitat type in the study area. In a confined mountainous area of Greece, the habitat-specific mean time to decay of roe deer pellet groups was estimated by locating and marking fresh pellet groups on several dates in the lead up to an FSC survey and returning to the marked signs at the time of the survey to record whether or not each pellet group had survived. Several logistic models were fitted to the data, and estimations were based on a multi-model inference (MMI) approach according to information theory. The highest mean time to decay was estimated in coniferous forests, while mid-ranged values were found in maquis shrubs, and the lowest mean time to decay was observed in open areas. MMI by model averaging, based on Akaike weights, is recommended for making robust parameter estimations and for dealing with uncertainty in model selection. © 2008 Springer-Verlag

Estimation of roe deer Capreolus capreolus and mouflon Ovis aries densities, abundance and habitat use in a mountainous Mediterranean area

The abundance, density, and habitat use of roe deer Capreolus capreolus (Linnaeus, 1758) and mouflon Ovis aries Linnaeus, 1758 were studied in a confined Mediterranean area in Greece with a dung survey based on the faecal accumulation rate (FAR) technique. Estimated density was modelled with generalized additive models using altitude, habitat type, and slope as potential covariates. Model selection among the set of candidate models was conducted based on their generalized cross-validation score. Roe deer had an estimated mean density of 13.9 ind./km2 and the best model included slope and habitat type as covariates. The mean density of mouflon in the study area was 22.1 ind./km2 and the best model used altitude and habitat type as covariates. For both species, the highest densities were encountered in abandoned cultivations and glades, followed by conifer forests, while the lowest densities were observed in maquis. However, use of open habitats by mouflon was much greater than it was for roe deer. The strong preference of mouflon (a grazer species) for open habitats that were abundant with grasses probably reflected food availability and contrasted with the more diverse habitat use by roe deer (a selective browser)

Brood sex ratio variation in a colonial raptor, the Eleonora's falcon, Falco eleonorae

Xirouchakis SM, Botsidou P, Baxevani K, Andreou G, Tsaparis D. Brood sex ratio variation in a colonial raptor, the Eleonora's falcon, Falco eleonorae. Animal Behaviour. 2023;195:93-106.Sex allocation theory predicts that species with reversed sexual size dimorphism frequently overproduce the cheapest sex at the brood level. A sex ratio deviation from parity is frequently documented among the offspring of raptors and is largely produced by sex-biased survival or parental adjustment as a response to environmental variability or demographic conditions. The Eleonora's falcon is a long-distance migrant wintering in Madagascar and southeast Africa and breeding colonially primarily in the Mediterranean Sea and the Canary Islands. It feeds on migratory passerines and thus depends greatly on the autumn migration flow and the prevailing winds. Being sexually size dimorphic (i.e. females are larger than males) and depending greatly on the migration, the species is a good case for investigating whether brood sex ratio variation is adaptive. In the present study, we examined the proportion of males and females reared during 2009–2020 in a falcon colony in southeast Crete (Greece) in relation to specific ecological and biological attributes. Female nestlings were shown to be costlier to produce as they are heavier than males. Overall, an unbiased sex ratio was observed across the years, although a consistent trend was recorded towards females early in the breeding season and first-hatched chicks and males late in the breeding season and third-hatched chicks. Our results provide strong evidence that parental condition, habitat quality and a brood reduction effect were the significant drivers for the observed sex ratio patterns. The overproduction of the costlier sex and a high survival of the cheaper one during food-rich years should be regarded as an adaptive evolutionary strategy of the species for maximizing its fitness returns per clutch and for maintaining a balanced offspring sex ratio in the population

New phylogeographic insights support the distinctiveness and conservation value of the little-known Greek roe deer populations

Despite their conservation status as Vulnerable and the need for targeted management actions, very little is actually known about the genetic diversity and phylogeography of the remnant populations of the roe deer (Capreolus capreolus) in Greece. In order to investigate these aspects we collected samples from nine locations in Greece and retrieved 80 sequences (834–836bp) for a fragment of the mtDNA control region. Analysis revealed high overall haplotype diversity, low nucleotide diversity and significant population structuring with site-specific haplotypes. In order to assign Greek roe deer haplotypes to previously identified haplogroups, we integrated our data with available roe deer sequences from across Europe. The analysis of the combined dataset showed that most of the haplotypes retrieved from Greek populations are novel, geographically confined and belong exclusively to the “Eastern” phylogeographic group. The indigenous populations of Greece are genetically distinct from other Balkan populations, which have a significant genetic component from the “Central” group. The Greek populations carry part of the ancestral gene pool of Late Pleistocene Balkan refugium, which has not contributed to the postglacial expansion of the species. The current phylogeographic pattern of roe deer in Greece seems to be the result of genetic drift due to habitat fragmentation and population decline. The genetic integrity of Greek roe deer should be maintained by avoiding uncontrolled reintroductions or translocations that could lead to admixture with allochthonous roe deer. © 2019 Deutsche Gesellschaft für Säugetierkund

New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies

Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)11 probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean number of alleles at 5.0 and mean observed heterozygosity at 0.520. The amplification success also in the nominotypical subspecies favours the use of these microsatellite loci in population genetic analyses as well as in the study of contact zones between smooth newt subspecies. © 2008 The Authors

A first step for sustainable breeding programmes in pikeperch (sander lucioperca) through the evaluation of the genetic variation in domesticated broodstocks and natural populations

The pikeperch is a temperate Eurasian freshwater/brackish water fish species with growing interest for the European aquaculture. Wild populations of pikeperch show signs of decline in many areas of its natural range of distribution (from Finland to the Aegean Sea, and East to the Aral and Caspian basins) due to human activities, such as the destruction of natural habitats and/or overfishing. The species has been introduced in northern Russia, Italy, Spain, Turkey, the North African countries (from Morocco to Tunisia) and many other regions. There are only a few commercial hatcheries that produce pikeperch in Europe. In principle, each farm uses its own stock, captured either from the wild or supplied by another farmer. Therefore, pikeperch populations differ from one farm to another depending upon the geographical origin of the captured wild populations, which were at the base of the captive stocks. The main objective of the present study was to develop and use highly informative and efficient for the species, multiplex panels of microsatellite loci, in order to assess the genetic variability of thirteen domesticated populations from commercial farms and of eight wild populations. In total, DNA from 971 fish samples (fin clips) was extracted using standard protocols. Two multiplexes (4-plex & 7-plex) were developed, optimized and finally used for genotyping of samples while all 21 populations were analyzed for basic population genetics parameters (allelic richness, heterozygosity indices, inbreeding coefficients). The genetic differentiation among locations was quantified by FST values. Genotyping of wild and domesticated populations and the comparative evaluation of their genetic status are extremely useful for the future establishment of genetic breeding programmes for sustainable optimal performance through domestication of pikeperch. Results indicate that most of the populations show medium to low levels of genetic diversity and some of them may be inbred. Differentiation between broodstocks was high in most cases, while lowest values were estimated for pairs of known common origin or geographic proximity

Fine scale spatial genetic structure of two syntopic newts across a network of ponds: Implications for conservation

In this study we used genetic approaches to assess the influence of landscape features on the dispersal patterns and genetic structure of two newt species (Triturus macedonicus and Lissotriton vulgaris) living syntopically in a network of ponds. Multilocus genotypes were used to detect and measure genetic variation patterns, population genetic structure and levels of gene flow. We interpret results on the basis of the different dispersal properties of the two species and explored the influence of certain landscape features, such as road and channel networks, on population connectivity. We found marked differences in the spatial genetic patterns of the respective species, which can be explained by their different dispersal properties. The road network seems to act as a barrier to dispersal in the overland dispersing L. vulgaris, while the channel network maintains connectivity in the aquatic dispersing T. macedonicus. The simultaneous and comparative consideration of species in a given area offers a much better understanding of the processes that govern population dynamics and persistence, providing valuable knowledge useful in conservation and management design. © 2013 Springer Science+Business Media Dordrecht

New polymorphic microsatellite loci for the Macedonian crested newt, Triturus macedonicus, and cross-priming testing in four other crested newt species

Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species. © 2008 The Authors