Spiros Papakostas

• University of Turku

The six6 and vgll3 genes play evolutionarily conserved roles in developmental processes and life history traits across species, including teleosts. Notable differences in genotype and allele frequencies of these genes have been observed between farmed and wild populations of European seabass and gilthead seabream, suggesting potential roles in trai...

The six6 and vgll3 genes play evolutionarily conserved roles in developmental processes and life history traits across species, including teleosts. Notable differences in genotype and allele frequencies of these genes have been observed between farmed and wild populations of European seabass and gilthead seabream, suggesting potential roles in trai...

Background: Runs of homozygosity (ROHs) and heterozygosity (ROHets) serve for the identification of genomic regions as candidates of selection, local adaptation, and population history. Methods: The present study aimed to comprehensively explore the ROH and ROHet patterns and hotspots in Greek native dairy goats, Eghoria and Skopelos, genotyped wit...

Genome scans provide a comprehensive method to explore genome‐wide variation associated with traits under study. However, linking individual genes to broader functional groupings and pathways is often challenging, yet crucial for understanding the evolutionary mechanisms underlying these traits. This task is particularly relevant for multi‐trait pr...

We investigated the prevalence and genetic diversity of Wolbachia pipientis strains in Aedes albopictus populations in Greece. Using a combination of PCR and Sanger sequencing techniques, we genotyped Wolbachia strains in 105 mosquitoes collected across eight different prefectures in 2021. We found a high prevalence of Wolbachia in both male (90%)...

Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age‐at‐maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domesticatio...

Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domesticatio...

Canine degenerative myelopathy (CDM) is a late-onset fatal disorder associated with a point mutation of the superoxide dismutase 1 (SOD1) gene (c.118G > A). The purpose of this study was to determine the genotype and allele frequencies of this mutation in 108 dogs, mainly in Belgian Malinois and German Shepherd dogs with (CDM-affected group) and wi...

The growth rate hypothesis (GRH) posits that the relative body phosphorus content of an organism is positively related to somatic growth rate, as protein synthesis, which is necessary for growth, requires P‐rich rRNA. This hypothesis has strong support at the interspecific level. Here, we explore the use of the GRH to predict microevolutionary resp...

In the face of the biodiversity crisis, concerted efforts towards understanding the effects of climate change and habitat loss and fragmentation, both locally and globally, are urgently needed. These are often attempted by leveraging the advances of modern genomics and bioinformatics methodologies. Especially in biodiversity hotspots, the need to u...

The identification of the genetic basis of domestication in fish species is of timely importance for the aquaculture industry in order to increase productivity, quality, and the welfare of farmed fish. The goal of this study is to investigate the largely unknown aquaculture-induced evolution in gilthead seabream, which is one of the most important...

Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylat...

The growth rate hypothesis, a central concept of Ecological Stoichiometry, explains the frequently observed positive association between somatic growth rate and somatic phosphorus content (P som ) in organisms across a broad range of taxa. Here, we explore its potential in predicting intraspecific microevolutionary adaptation. For this, we subjecte...

We present an updated checklist of the rotifer fauna from inland aquatic habitats in continental Ecuador and the Galápagos islands based on published rotifer records found in the literature. The checklist summarizes the status of the current taxonomic and faunistic knowledge on rotifers in Ecuador, updates the nomenclature, and reports the regions...

The authors of the original publication recognized that, for three of the clones (MAN-L5, LFL2, KOR), the data of two of the raw morphometric measurements contained in Supplementary Material 2 of the article were flipped (the distance between the anterior tips of the 3rd dorsal spines ‘b’ and the width of the lorica ‘c’). The corrected Supplementar...

(1) Brachionus calyciflorus is arguably the most studied freshwater monogonont rotifer. Although it has been recognized as a cryptic species complex for more than a decade, a formal (re-)description of the four species known so far (B. calyciflorus, B. dorcas, B. elevatus and B. fernandoi) has only recently been made. Information on the ecology of...

The presence of the rotifer species Brachionus rotundiformis from the B. plicatilis species complex in Lake Arcturo, a saline lake in the Genovesa Island of the Galápagos Islands, is here reported. This is the first record of the species for the rotifer fauna of Ecuador as well as of the species complex to the Galápagos Islands. This finding is con...

Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one...

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological...

Records of Brachionus calyciflorus synonyms. (DOCX)

Classification functions of the stepwise discriminant analysis performed on species ‘B’, ‘C’, and ‘D’. (DOCX)

Amount of morphometric variation explained by species identity for each pair of the investigated species. (DOCX)

Classification functions of the stepwise discriminant analysis performed on species ‘A’, ‘B’, ‘C’, and ‘D’. (DOCX)

Summary statistics for the selection of morphometric traits measured on individuals of the four species. (DOCX)

Monogononta is the most speciose class of rotifers, with more than 2000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex, an...

Discordance between mitochondrial and nuclear phylogenies is being increasingly recognized in animals and may confound DNA-based taxonomy. This is especially relevant for taxa whose microscopic size often challenges any effort to distinguish between cryptic species without the assistance of molecular data. Regarding mitonuclear discordance, two str...

Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying...

Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying...

Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is b...

A better understanding of the ability of organisms to adapt to local selection conditions is essential for a better insight in their ecological dynamics. The study of micro-evolutionary adaptation and its eco-evolutionary consequences is challenging for many reasons and the choice of a suitable model organism is particularly important. In this pape...

Three well-defined groups, consisting of 15 species, have recently been ascribed to organisms historically identified as the Brachionus plicatilis species complex. One of these groups, the large clade, is composed of two named species (Brachionus plicatilis s.s. and Brachionus manjavacas) and two species identifiers (B. ‘Nevada’ and B. ‘Austria’)....

Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relatio...

Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relatio...

Understanding how populations adapt to changing environmental conditions is a long-standing theme in evolutionary biology. Gene expression changes have been recognized as an important driver of local adaptation, but relatively little is known regarding the direction of change and in particular, about the interplay between plastic and evolutionary g...

Humans alter biogeochemical cycles of essential elements such as phosphorus (P). Prediction of ecosystem consequences of altered elemental cycles requires integration of ecology, evolutionary biology and the framework of ecological stoichiometry. We studied micro-evolutionary responses of a herbivorous rotifer to P-limited food and the potential co...

Brachionus sessilis Varga, 1951 is an epizoic rotifer living exclusively on cladocerans of the genus Diaphanosoma. Current taxonomic knowledge relies solely on limited morphological information, whereas there is no type material. Here, we aim to resolve issues concerning its morphology and taxonomy using both morphological and genetic characters on...

Understanding the factors that shape the evolution of gene expression is a central goal in biology, but the molecular mechanisms behind this remain controversial. A related major goal is ascertaining how such factors may affect the adaptive potential of a species or population. Here we demonstrate that temperature-driven gene expression changes in...

Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains chal...

The life cycle of cyclical parthenogens provides a unique model for the study of spatiotemporal microevolutionary processes at ecologically relevant time scales. Considerable effort has been invested to understand spatial population structure, but critical information is still missing on temporal population divergence. This study aims to provide in...

Osmoregulation is a vital physiological function for fish, as it helps maintain a stable intracellular concentration of ions in environments of variable salinities. We focused on a primarily freshwater species, the European whitefish (Coregonus lavaretus), to investigate the molecular mechanisms underlying salinity tolerance and examine whether the...

Aim We focus on the biogeographical role of the Balkan Peninsula as a glacial refugium and source of northward post-glacial dispersal for many European taxa. Specifically, we analysed the genetic structure and variation of wild boar (Sus scrofa) samples primarily from Greece, a region that has repeatedly served as a glacial refugium within the Balk...

Asexual organisms are confronted with substantial drawbacks, both immediate and delayed, threatening their evolutionary persistence. Yet, genetic associations with asexuality may refresh the gene pool promoting adaptation of clonal lineages; polyploidy is one of them. Parthenogenesis itself and/or polyploidy are responsible for the maintenance and...

Salmonids are teleost fish of profound research and economic interest. Embryonic development is a key aspect of salmonid biology that can be critically affected by environmental parameters. Still, their proteome during embryogenesis remains largely unexplored. This study investigates the proteome of the eyed-egg and hatching stages of embryonic dev...

The recent application of different molecular techniques to Brachionus plicatilis hatchery strains has revealed the presence of five members of what is now known as the B. plicatilis complex of cryptic species and has offered new perspectives to the aquaculture industry via a genetically-oriented strain management. In this work, we have employed th...

Cryptic species are increasingly being recognized in many organisms. In Brachionus rotifers, many morphologically similar yet genetically distinct species/biotypes have been described. A number of Brachionus cryptic species have been recognized among hatchery strains. In this study, we present a simple, one-step genetic method to detect the presenc...

Many zooplanktonic organisms, like the cyclic parthenogenetic rotifer Brachionus plicatilis (Rotifera: Monogononta), are actually a complex of species and biotypes with a high degree of morphological similarity (i.e. cryptic species). Various phylogenetic studies with molecular markers (e.g. ITS1 and COI) on wild Brachionus populations described th...

Brachionus sp. rotifers are widely used in large numbers for larval rearing in fish industry. By practice, cultured rotifers are discriminated on the basis of their body size. Recently however, marked polymorphism has been uncovered with the use of molecular markers. Rotifers of the same size but of distinct genetic profiles have been shown to diff...

The marine finfish industry worldwide depends greatly on the mass culture of Brachionus rotifers. Recently, molecular data have revealed a more complicated view about the species status of Brachionus rotifers than previous mainly morphological assessments. Under this view, Brachionus rotifers are comprised of many morphologically similar, albeit ge...

Few efforts have dealt with the genetic make up of the Brachionus plicatilis rotifers which are often used as live feed in the larviculture of many marine fish. Recent results have demonstrated that the B. plicatilis species is actually a species complex. In this study a number of molecular markers (Restriction Fragment Length Polymorphism (RFLP) a...

Recent reports indicate an extensive amount of molecular evolution separating cryptic taxa as well as significant population structure at a microgeographical scale. Appropriate molecular markers are particularly suitable for distinguishing cryptic biological species. In this study, we examine the phylogenetic utility of 16S rRNA in elucidating the...