Riho Gross

RESEARCH, TEACHING, or OTHER INTERESTS

Agricultural and Biological Sciences, Aquatic Science, Ecology, Evolution, Behavior and Systematics, Animal Science and Zoology

Scopus Publications

Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch
María‐Eugenia López, Mikhail Ozerov, Lilian Pukk, Kristina Noreikiene, Riho Gross, and Anti Vasemägi
Wiley
ABSTRACTHow genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free‐living species still lack a comprehensive understanding of the primary molecular mechanisms of adaptation. Here, we characterised the targets of selection associated with drastically different aquatic environments—humic and clear water—in the common freshwater fish, Eurasian perch (Perca fluviatilis). By using whole‐genome sequencing (WGS) on a large population dataset (n = 42 populations) and analysing 873,788 SNPs, our primary aim was to uncover novel and confirm known footprints of selection. We compared individual and pooled WGS, and developed a novel approach, termed dynamic outlier slicing, to assess how the choice of outlier‐calling stringency influences functional and Gene Ontology (GO) enrichment. By integrating genome‐environment association (GEA) analysis with allele frequency‐based approaches, we estimated composite selection signals (CSS) and identified 2679 outlier SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic outlier slicing identified robust enrichment signals in five annotation categories (upstream, downstream, synonymous, 5′UTR and 3′UTR) highlighting the crucial role of regulatory elements in adaptive evolution. Furthermore, GO analyses revealed strong enrichment of molecular functions associated with gated channel activity, transmembrane transporter activity and ion channel activity, emphasising the importance of osmoregulation and ion balance maintenance. Our findings demonstrate that despite substantial random drift and divergence, WGS of high number of population pools enabled the identification of strong selection signals associated with adaptation to both humic and clear water environments, providing robust evidence of widespread adaptation. We anticipate that the dynamic outlier slicing method we developed will enable a more thorough exploration of adaptive divergence across a diverse range of species.


Integrative Genomics Refines Tissues, Candidate Genes and Putative Regulatory Links Involved in the Humic Adaptation of Keystone Freshwater Fish
M. Yu. Ozerov, K. Noreikiene, K. Taube, R. Gross, and A. Vasemägi
Wiley
ABSTRACTAlthough population genomics approaches have been successful in identifying regions of the genome shaped by natural selection, progress in dissecting the molecular mechanisms of adaptive variants and traits has been slow. By integrating multi‐tissue (gill, spleen, olfactory rosette, whole eye, and liver) transcriptomes from 16 wild Eurasian perch (Perca fluviatilis) populations and previously identified footprints of selection, we prioritise tissues, candidate genes, and putative SNP‐gene expression associations potentially involved in the humic adaptation of this keystone freshwater fish. Over 5000 differentially expressed genes (DEGs) were discovered across the five tissues. A significant excess of outlier SNPs among DEGs found in the gill and spleen tissues indicated their potential involvement in humic adaptation. Next, we identified 2640 cis‐eQTLs, and observed significant enrichment of outliers among expression‐associated SNPs (eSNPs) in spleen and olfactory rosette tissues, as well as in all tissues combined. Several eQTLs were found in the regions showing the strongest signals of selection, which also harboured DEGs (chr. 5: PLAGL2, chr. 7: PPP1R8, TCHH). Thus, our integrative analyses enabled us to pinpoint specific organs that potentially play a key role in adaptation, prioritise candidate genes under divergent selection based on their expression patterns, and identify links between SNPs and transcript abundance variation. We expect that by combining evolutionary and functional genomics perspectives this work provides a practical framework for understanding the genetic basis of phenotypic diversification and adaptation across a wide range of species.


Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch
Vitalii Lichman, Mikhail Ozerov, María‐Eugenia López, Kristina Noreikiene, Siim Kahar, Lilian Pukk, Oksana Burimski, Riho Gross, and Anti Vasemägi
Wiley
AbstractThe contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole‐genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000–100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome‐wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data‐mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.


Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking
Oksana Burimski, Anti Vasemägi, and Riho Gross
Springer Science and Business Media LLC
AbstractSeveral countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders (Nb) over the study period. Furthermore, we found that immigration rates (m) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation.


Spatial and intra-host distribution of myxozoan parasite Tetracapsuloides bryosalmonae among Baltic sea trout (Salmo trutta)
Magnus Lauringson, Siim Kahar, Taigor Veevo, Maidu Silm, Duncan Philpott, Roland Svirgsden, Mehis Rohtla, Priit Päkk, Riho Gross, Tanel Kaart,et al.
Wiley
AbstractProliferative kidney disease caused by the myxozoan parasite Tetracapsuloides bryosalmonae has been actively studied in juvenile salmonids for decades. However, very little is known about parasite prevalence and its geographical and intra‐host distribution at older life stages. We screened T. bryosalmonae among adult sea trout (Salmo trutta) (n = 295) collected along the Estonian Baltic Sea coastline together with juvenile trout from 33 coastal rivers (n = 1752) to assess spatial infection patterns of the adult and juvenile fish. The parasite was detected among 38.6% of adult sea trout with the prevalence increasing from west to east, and south to north, along the coastline. A similar pattern was observed in juvenile trout. Infected sea trout were also older than uninfected fish and the parasite was detected in sea trout up to the age of 6 years. Analysis of intra‐host distribution of the parasite and strontium to calcium ratios from the otoliths revealed that (re)infection through freshwater migration may occur among adult sea trout. The results of this study indicate that T. bryosalmonae can persist in a brackish water environment for several years and that returning sea trout spawners most likely contribute to the parasite life cycle by transmitting infective spores.


Integrating population genetics and species distribution modelling to guide conservation of the noble crayfish, Astacus astacus, in Croatia
Leona Lovrenčić, Martina Temunović, Riho Gross, Marin Grgurev, and Ivana Maguire
Springer Science and Business Media LLC
AbstractThe noble crayfish, Astacus astacus, is an indigenous European freshwater species. Its populations show significant declines caused by anthropogenic pressure on its habitats, climate change and the spread of invasive species. Diminishing populations’ trends and loss of genetic diversity highlight the need for effective conservation that will ensure their long-term survival. We combined population genetics and species distribution modelling (SDM) to reveal the impact of climate change and invasive species on the noble crayfish, and to guide future conservation programs of current populations. Our study showed that Croatian populations of A. astacus harbour an important part of species genetic diversity and represent significant genetic reservoir at the European level. The SDM results predicted substantial reductions of suitable habitats for A. astacus by the 2070; only 13% of its current potential distribution is projected to remain stable under pessimistic Representative Concentration Pathway (RCP 8.5) emission scenario. Moreover, most of the populations with high genetic diversity are located in the areas predicted to become unsuitable, and consequently have a high probability of being lost in the future. Further, SDM results also indicated considerable decrease of future habitat suitability for invasive crayfish species in Croatia, suggesting that climate change poses a major threat to already endangered A. astacus. The obtained results help in the identification of populations and areas with the highest conservation value which should be given the highest priority for protection. In order to preserve present diversity in areas that are predicted as suitable, we propose assisted migration and repopulation approaches, for enhancing populations’ size and saving maximum genetic variability. The result of our research emphasizes once again the benefits of multidisciplinary approach in the modern biodiversity conservation.


Temporally stable small-scale genetic structure of Northern pike (Esox lucius) in the coastal Baltic Sea
Alfonso Diaz-Suarez, Kristina Noreikiene, Veljo Kisand, Oksana Burimski, Roland Svirgsden, Mehis Rohtla, Mikhail Ozerov, Riho Gross, Markus Vetemaa, and Anti Vasemägi
Elsevier BV



Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch
Mikhail Ozerov, Kristina Noreikiene, Siim Kahar, Magnus Huss, Ari Huusko, Toomas Kõiv, Margot Sepp, María‐Eugenia López, Anna Gårdmark, Riho Gross,et al.
Wiley
AbstractExtreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost “nocturnal” environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic‐associated selection, we performed whole‐genome sequencing of perch originating from 16 humic and 16 clear‐water lakes in northern Europe. We identified over 800,000 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole‐genome analysis to illuminate the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.


Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers
Riho Gross, Leona Lovrenčić, Mišel Jelić, Frederic Grandjean, Simona Ðuretanović, Vladica Simić, Oksana Burimski, Lena Bonassin, Marius-Ioan Groza, and Ivana Maguire
PeerJ
Background The noble crayfish (Astacus astacus) is a native European species in decline, with a contracting range and diminishing populations and abundance. Previous studies revealed this species significant genetic diversity in the south-eastern Europe, with populations from the western and the southern part of the Balkan Peninsula being the most divergent. However, sampling of populations from the western part of the Balkans was limited and insufficient for investigating genetic diversity and population divergence for the purpose of conservation planning and management. Thus, the major aim of this study was to fill in this knowledge gap by studying mitochondrial and microsatellite DNA diversity, using 413 noble crayfish from 18 populations from waterbodies in the western part of the Balkan Peninsula. Methods Phylogenetic analysis of studied populations and their mitochondrial diversity were studied using COI and 16S sequences and population genetic structure was described using 15 microsatellite loci. Results Phylogeographic analysis revealed new divergent mitochondrial haplotypes for the populations in the westernmost part of the Balkan Peninsula in the tributaries of the Sava and Drava rivers. Microsatellite data indicated that these populations harbour an important component of genetic diversity within A. astacus. The results suggest that the western part of the Balkans played an important role as microrefugia during the Pleistocene climate fluctuations, allowing the long term persistence of A. astacus populations in this region. These results will also be important to supporting conservation decision making and planning.


Climate change-driven disease in sympatric hosts: Temporal dynamics of parasite burden and proliferative kidney disease in wild brown trout and Atlantic salmon
Magnus Lauringson, Ilkka Nousiainen, Siim Kahar, Oksana Burimski, Riho Gross, Tanel Kaart, and Anti Vasemägi
Wiley
AbstractGlobal climate change is altering the abundance and spread of various parasites, which has important consequences not only for host–parasite interactions but also for the relationships between different host species. Here, we focus on the myxozoan endoparasite Tetracapsuloides bryosalmonae that causes temperature‐dependent proliferative kidney disease (PKD) in salmonids. We characterized the temporal changes in the parasite load and the severity of PKD signs (renal hyperplasia, haematocrit) in two sympatric populations of wild brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). We found that both the parasite load and disease signs vary considerably between individuals, species, rivers and sampling periods. We showed that Atlantic salmon was able to slow down the initial parasite proliferation rate and subsequently tolerate high parasite burden without obvious disease signs. In contrast, the initial parasite proliferation rate was much higher in brown trout, which was followed by the development of severe PKD signs. Thus, the speed of parasite proliferation, rather than the absolute number of the parasites in the host kidney, may play an important role in interspecific variation in PKD susceptibility. To conclude, this study illustrates the usefulness of temporal perspective for understanding host defence mechanisms and climate change‐mediated impacts in the wild.


First record of an established marbled crayfish Procambarus virginalis (Lyko, 2017) population in Estonia
Fabio Ercoli
Regional Euro-Asian Biological Invasions Centre Oy (REABIC)
Invasive marbled crayfish Procambarus virginalis (Lyko, 2017) is spreading alarmingly fast across European countries and beyond. Early maturation, parthenogenetic reproduction mode and high growth rate contribute to a high potential invasiveness. Marbled crayfish can pose severe effects on native communities impacting the native crayfish populations being carrier of the crayfish plague disease caused by Aphanomyces astaci. Here we report the first record of marbled crayfish in Estonia. In total, 104 individuals were found in the artificially warm outflow channel of the cooling system of Balti Power Plant, entering to the water reservoir of the River Narva. Molecular analyses confirmed the morphological identification of captured specimens as a marbled crayfish. Four out of six marbled crayfish individuals exhibited the presence of crayfish plague agent, though at very low level. This suggests that marbled crayfish can potentially be a new vector of crayfish plague in Estonian freshwater ecosystems containing native noble crayfish Astacus astacus populations. Monitoring and eradication actions are urgently needed not only in the outflow channel where the species was found but in the whole water reservoir and River Narva itself.


Highly continuous genome assembly of eurasian perch (perca fluviatilis) using linked-read sequencing
Mikhail Yu Ozerov, Freed Ahmad, Riho Gross, Lilian Pukk, Siim Kahar, Veljo Kisand, and Anti Vasemägi
Oxford University Press (OUP)
Abstract The Eurasian perch (Perca fluviatilis) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome ∼1.0 Gbp assembly (scaffold N50 = 6.3 Mb; the longest individual scaffold of 29.3 Mb; BUSCO completeness of 88.0%), which included 281.6 Mb of putative repeated sequences. The perch genome assembly presented here, generated from small amount of starting material (0.75 ng) and a single linked-read library, is highly continuous and considerably more complete than the currently available draft of P. fluviatilis genome. A total of 23,397 protein-coding genes were predicted, 23,171 (99%) of which were annotated functionally from either sequence homology or protein signature searches. Linked-read technology enables fast, accurate and cost-effective de novo assembly of large non-model eukaryote genomes. The highly continuous assembly of the Eurasian perch genome presented in this study will be an invaluable resource for a range of genetic, ecological, physiological, ecotoxicological, functional and comparative genomic studies in perch and other fish species of the Percidae family.


Genetic analysis reveals the diversity of larval Gobiidae in a temperate estuary
H. Ojaveer, R. Gross, K. Laur, T. Arula, and R. Klais
Wiley
Using molecular tools to examine Gobiidae, the second most abundant taxon in ichthyoplankton samples in the Gulf of Riga (Baltic Sea), the sand goby Pomatoschistus minutus was the most abundant taxon (82% of all individuals analysed), the common goby Pomatoschistus microps constituted 12% and the black goby Gobius niger 6%. The spatiotemporal distribution of P. microps and G. niger indicated a preference for habitats closer to the river inlet and their abundances increased slightly towards the end of the sampling period in summer. The species composition was interpreted in the context of the prevailing habitat conditions, characterized by extremely low water transparency, low salinity, limited spread of vegetated area and dominance of sandy–muddy substrata.


Development and characterization of novel tetranucleotide microsatellite markers in the noble crayfish (Astacus astacus) suitable for highly multiplexing and for detecting hybrids between the noble crayfish and narrow-clawed crayfish (A. leptodactylus)
Riho Gross, Kuldar Kõiv, Lilian Pukk, and Katrin Kaldre
Elsevier BV



Quantitative genetic variation in, and environmental effects on, pathogen resistance and temperature-dependent disease severity in a wild trout
Paul Vincent Debes, Riho Gross, and Anti Vasemägi
University of Chicago Press
Health after pathogen contact varies among individuals because of differences in pathogen load (which is limited by resistance) and disease severity in response to pathogen load (which is limited by tolerance). To understand pathogen-induced host evolution, it is critical to know not only the relative contributions of nongenetic and genetic variation to resistance and tolerance but also how they change environmentally. We quantified nongenetic and genetic variation in parasite load and the associated temperature-dependent disease among trout siblings from two rivers. We detected a genetic variance for parasite load 6.6 times as large in the colder river. By contrast, genetic variance for disease traits tended to be larger in the warmer river, where the disease was manifested more severely. The relationships between disease severity and pathogen load (tolerance) exhibited plateaus at low pathogen load and stronger steepening slopes at high pathogen load in the warmer river. Our study demonstrates the environmental influence on disease severity, nongenetic and genetic variance for health-damage-limiting host abilities, and the shape of tolerance curves. Environmental variability is predicted to govern the presence and intensity of selection, change the relative contributions of nongenetic and genetic variance, and therefore hamper evolution toward more resistant and tolerant hosts.


Parasite infection and decreased thermal tolerance: impact of proliferative kidney disease on a wild salmonid fish in the context of climate change
Matthieu Bruneaux, Marko Visse, Riho Gross, Lilian Pukk, Lauri Saks, and Anti Vasemägi
Wiley
Summary Parasites and pathogens can have an important effect on their host's thermal resistance. The impact of parasite infection on host physiological performances has traditionally been studied in controlled laboratory conditions, and much less is known about its actual effects in wild populations. Nonetheless, such knowledge is critical when assessing the effect of climate change on the future survival of the host. Tetracapsuloides bryosalmonae is a myxozoan endoparasite causing proliferative kidney disease (PKD) in salmonids. Infection and clinical symptoms of PKD are dependent on environmental temperature and PKD has become an emerging disease of primary importance for farmed and wild salmonids in the last decades. Despite important achievements in understanding PKD pathology in recent years, there are still crucial gaps in the knowledge of the disease ecology, notably in how the parasite affects host performance in the wild. We sampled juvenile (0+) brown trout (Salmo trutta) from the wild during early and late summer and assessed relative parasite load (DNA quantification with qPCR) and disease severity (kidney hyperplasia). We also measured haematocrit, leucocyte formula, aerobic scope and upper thermal tolerance in a field‐physiology approach in order to better understand the relationships between PKD severity and host performance. By using wild‐caught individuals and performing measurements directly on location, we aimed to gain insights into host physiology in a natural environment while avoiding biases caused by laboratory acclimation. We found that most physiopathological symptoms in the wild were strongly correlated with kidney hyperplasia, but more weakly linked to parasite load. Disease severity was positively correlated with anaemia and abundance of circulating thrombocytes, and negatively correlated with aerobic scope and thermal tolerance. Our results suggest that impaired aerobic performances and thermal tolerance in infected fish may potentially result in decreased host survival in the wild, especially in relation with predicted higher average summer temperatures and increased frequency of extreme events (summer heatwaves) in the context of global climate change. A Lay Summary is available for this article.


Genetic discrimination of brackish and freshwater populations of Eurasian perch (Perca fluviatilis L.) in the Baltic Sea drainage: Implications for fish forensics
Lilian Pukk, Riho Gross, Markus Vetemaa, and Anti Vasemägi
Elsevier BV



Outlier loci detect intraspecific biodiversity amongst spring and autumn spawning herring across local scales
Dorte Bekkevold, Riho Gross, Timo Arula, Sarah J. Helyar, and Henn Ojaveer
Public Library of Science (PLoS)
Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and compared the results with data for autumn spawning North Sea herring. Temporally replicated analyses reveal clear genetic differences between ecotypes and hence support reproductive isolation. Loci showing non-neutral behaviour, so-called outlier loci, show convergence between autumn spawning herring from demographically disjoint populations, potentially reflecting selective processes associated with autumn spawning ecotypes. The abundance and exploitation of the two ecotypes have varied strongly over space and time in the Baltic Sea, where autumn spawners have faced strong depression for decades. The results therefore have practical implications by highlighting the need for specific management of these co-occurring ecotypes to meet requirements for sustainable exploitation and ensure optimal livelihood for coastal communities.


Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases
M. Y. Ozerov, R. Gross, M. Bruneaux, J.‐P. Vähä, O. Burimski, L. Pukk, and A. Vasemägi
Wiley
AbstractMany salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery‐reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts of inadvertent gene flow via straying from hatchery releases on wild populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16 years (1996–2012). Both microsatellites and SNPs revealed congruent population genetic structuring, indicating that introgression changed the genetic make‐up of wild populations by increasing genetic diversity and reducing genetic divergence. However, the degree of genetic introgression varied among studied populations, being higher in the eastern part and lower in the western part of Estonia, which most likely reflects the history of past stocking activities. Using kernel smoothing and permutation testing, we detected considerable heterogeneity in introgression patterns across the genome, with a large number of regions exhibiting nonrandom introgression widely dispersed across the genome. We also observed substantial variation in nonrandom introgression patterns within populations, as the majority of genomic regions showing elevated or reduced introgression were not consistently detected among temporal samples. This suggests that recombination, selection and stochastic processes may contribute to complex nonrandom introgression patterns. Our results suggest that (i) some genomic regions in Atlantic salmon are more vulnerable to introgressive hybridization, while others show greater resistance to unidirectional gene flow; and (ii) the hybridization of previously separated populations leads to complex and dynamic nonrandom introgression patterns that most likely have functional consequences for indigenous populations.


Less is more: Extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology
Lilian Pukk, Freed Ahmad, Shihab Hasan, Veljo Kisand, Riho Gross, and Anti Vasemägi
Wiley
AbstractMassively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction‐site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare‐cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols.


The effect of two different feeds on growth, carapace colour, maturation and mortality in marbled crayfish (Procambarus fallax f. virginalis)
Katrin Kaldre, Kerli Haugjärv, Mari Liiva, and Riho Gross
Springer Science and Business Media LLC



Wild Estonian and Russian sea trout (Salmo trutta) in Finnish coastal sea trout catches: Results of genetic mixed-stock analysis
Marja-Liisa Koljonen, Riho Gross, and Jarmo Koskiniemi
Springer Science and Business Media LLC
For responsible fisheries management of threatened species, it is essential to know the composition of catches and the extent to which fisheries exploit weak wild populations. The threatened Estonian, Finnish and Russian sea trout populations in the Gulf of Finland are targets of mixed-stock fisheries. The fish may originate from rivers with varying production capacities, from different countries, and they may also have either a wild or hatchery origin. In order to resolve the composition of Finnish coastal sea trout catches, we created a standardized baseline dataset of 15 DNA microsatellite loci for 59 sea trout populations around the Gulf of Finland and tested its resolution for mixed-stock analysis of 1372 captured fish. The baseline dataset provided sufficient resolution for reliable mixture analysis at regional group level, and also for most of the individual rivers stocks. The majority (76-80%) of the total catch originated from Finnish sea trout populations, 6-9% came from Russian and 12-15% from Estonian populations. Nearly all Finnish trout in the catch were of hatchery origin, while the Russian and Estonian trout were mostly of wild origin. The proportion of fish in the Finnish catches that originated from rivers with natural production was at least one fifth (22%, 19-23%). Two different spotting patterns were observed among the captured trout, with a small and sparsely spotted form being markedly more common among individuals of Russian (28%) and Estonian origin (22%) than among fish assigned to a Finnish origin (0.7%).


Double-restriction-site-associated DNA (dRAD) approach for fast microsatellite marker development in Eurasian perch (Perca fluviatilis L.)
Lilian Pukk, Veljo Kisand, Freed Ahmad, Riho Gross, and Anti Vasemägi
Springer Science and Business Media LLC



Microsatellite markers reveal clear geographic structuring among threatened noble crayfish (Astacus astacus) populations in Northern and Central Europe
Riho Gross, Stefan Palm, Kuldar Kõiv, Tore Prestegaard, Japo Jussila, Tiit Paaver, Juergen Geist, Harri Kokko, Anna Karjalainen, and Lennart Edsman
Springer Science and Business Media LLC



Genetic and life-history changes associated with fisheries-induced population collapse
Lilian Pukk, Anna Kuparinen, Leili Järv, Riho Gross, and Anti Vasemägi
Wiley
AbstractOver the recent years, growing number of studies suggests that intensive size‐selective fishing can cause evolutionary changes in life‐history traits in the harvested population, which can have drastic negative effects on populations, ecosystems and fisheries. However, most studies to date have overlooked the potential role of immigration of fish with different phenotypes as an alternative plausible mechanism behind observed phenotypic trends. Here, we investigated the evolutionary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24‐year period. We detected marked changes in size‐ and age‐distributions and increase in juvenile growth rate. We also observed reduction of age at sexual maturity in males that has frequently been considered to support the hypothesis of fisheries‐induced evolution. However, combined individual‐based life‐history and genetic analyses indicated increased immigration of foreign individuals with different life‐history patterns as an alternative mechanism behind the observed phenotypic change. This study demonstrates the value of combining genetic and phenotypic analyses and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations.