Riho Gross
@emu.ee
Institute of Veterinary Medicine and Animal Science
Estonian University of Life Sciences
RESEARCH, TEACHING, or OTHER INTERESTS
Agricultural and Biological Sciences, Aquatic Science, Ecology, Evolution, Behavior and Systematics, Animal Science and Zoology
Scopus Publications
Scopus Publications
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.
Alfonso Diaz-Suarez, Kristina Noreikiene, Veljo Kisand, Oksana Burimski, Roland Svirgsden, Mehis Rohtla, Mikhail Ozerov, Riho Gross, Markus Vetemaa, and Anti Vasemägi
Elsevier BV
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.
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.
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.
Riho Gross, Kuldar Kõiv, Lilian Pukk, and Katrin Kaldre
Elsevier BV
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.
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.
Lilian Pukk, Riho Gross, Markus Vetemaa, and Anti Vasemägi
Elsevier BV
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.
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.
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.
Katrin Kaldre, Kerli Haugjärv, Mari Liiva, and Riho Gross
Springer Science and Business Media LLC
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%).
Lilian Pukk, Veljo Kisand, Freed Ahmad, Riho Gross, and Anti Vasemägi
Springer Science and Business Media LLC
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
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.
MV Ozerov, J Lumme, P Päkk, P Rintamäki, MS Ziętara, Y Barskaya, D Lebdeva, E Saadre, R Gross, CR Primmer,et al.
Inter-Research Science Center
We describe an unusually high infection rate of Gyrodactylus salaris Malmberg in juvenile Atlantic salmon Salmo salar L. of Baltic Sea origin, which are generally believed to be more resistant to G. salaris than East Atlantic salmon populations. Based on analyses of mitochondrial (complete cytochrome oxidase 1 [CO1] gene, 1548 bp) and nuclear (ADNAM1, 435 bp; internal transcribed spacer [ITS] rDNA region, 1232 bp) DNA fragments, the closest relatives of the characterized Estonian G. salaris strain were parasites found off the Swedish west coast and in Raasakka hatchery, Iijoki (Baltic Sea, Finland). Analyses of 14 microsatellite loci of the host S. salarrevealed that approximately 40% of studied fish were triploids. We subsequently identified triploid Atlantic salmon of Baltic origin as more susceptible to G. salaris infection than their diploid counterparts, possibly due to compromised complement-dependent immune pathways in triploid salmon. This is in accordance with earlier studies that have shown elevated susceptibility of triploids to various viral or bacterial pathogens, and represents one of the first reports of increased susceptibility of triploid salmonid fish to an ectoparasite. However, further experimental work is needed to determine whether triploid Atlantic salmon is generally more susceptible to G. salaris compared to their diploid counterparts, irrespective of the particular triploidization method and population of origin.
Anti Vasemägi, Riho Gross, Daniel Palm, Tiit Paaver, and Craig R Primmer
Springer Science and Business Media LLC
B. GUM, R. GROSS, and J. GEIST
Wiley
Abstract European grayling, Thymallus thymallus (L.), populations have steadily declined since the mid‐1980s, mostly because of habitat degradation and increased predation pressure. To provide guidelines for conservation strategies and future management programmes, delineation of conservation and management units is warranted. Over the last decade, several studies have investigated the phylogeography and population genetic structure of T. thymallus using mitochondrial and nuclear microsatellite DNA markers. However, no study has covered the distribution range of T. thymallus across Europe; thus, a comprehensive survey of the evolutionary history of the species is lacking. This paper synthesises the major findings of the molecular studies and provides guidelines for the conservation and management of genetic resources of T. thymallus. At least five major mtDNA lineages have evolved in geographical isolation during the Pleistocene and these lineages should be recognised as the basic evolutionary significant units for T. thymallus in northern, central and southern Europe. There is also evidence for a high level of admixture among major lineages and sublineages, especially in the contact zones of drainages (e.g. in mainland Sweden and Norway and in central Germany), most probably resulting from a complex process of post‐glacial and inter‐glacial colonisation and re‐colonisation events from different refugia during the Pleistocene ice ages. Based on the microsatellite data, T. thymallus shows a substantial level of inter‐population genetic differentiation and, compared with other freshwater fish species, a relatively low level of within‐population genetic diversity. The species develops discrete population structure, both within hydrologically connected rivers or lakes on comparatively small scales as well as in large river systems.
Aurelija Samuiloviene, Antanas Kontautas, and Riho Gross
Springer Science and Business Media LLC
K. Kõiv, R. Gross, T. Paaver, M. Hurt, and R. Kuehn
Wiley
Description: Noble crayfish (Astacus astacus L.) is the most common and the most highly appreciated freshwater crayfish species in Europe. Once abundant, it is now listed as vulnerable by the IUCN Red List of Threatened Species, and there is increased interest in the aquaculture of this species for stocking and consumption purposes. Allozyme studies revealed little variation in A. astacus and stressed the need for the development of more informative microsatellite markers. We report here the isolation and characterization of 11 polymorphic microsatellite markers that, together with eight loci from our previous study, allow us to assess and monitor genetic variation in natural and farmed populations of A. astacus.
Kuldar Kõiv, Riho Gross, Tiit Paaver, and Ralph Kuehn
Springer Science and Business Media LLC
Riho Gross, Priit Lulla, and Tiit Paaver
Elsevier BV
T. L. King, E. Verspoor, A. P. Spidle, R. Gross, R. B. Phillips, M‐L. Koljonen, J. A. Sanchez, and C. L. Morrison
Wiley