1
|
Ragauskas A, Ignatavičienė I, Rakauskas V, Grauda D, Prakas P, Butkauskas D. Trends of Eurasian Perch ( Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene. Animals (Basel) 2023; 13:3057. [PMID: 37835663 PMCID: PMC10571732 DOI: 10.3390/ani13193057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability and microevolution of Perca fluviatilis within phylogeographic and anthropogenic contexts. We sequenced a 627 bp fragment encompassing the ATP6 region and used it for genetic analysis of 193 perch caught in Latvia, Lithuania, Belarus, and Ukraine, representing natural and anthropogenically impacted populations. We evaluated patterns of intraspecific genetic diversity in the ATP6 region and phylogeographic trends within the studied area compared with previously established D-loop trends. Evaluation of ATP6 coding sequence variability revealed that among 13 newly detected haplotypes, only two were caused by non-synonymous substitutions of amino acids of the protein. PCoA revealed three genetic groups (I-III) based on the ATP6 region that encompassed four previously described genetic groups established based on the mtDNA D-loop. The two mtDNA regions (D-loop and ATP6) have microevolved at least partially independently. Prolonged anthropogenic impacts may generate new point mutations at the ATP6 locus, but this phenomenon could be mainly concealed by natural selection and reparation processes.
Collapse
Affiliation(s)
- Adomas Ragauskas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Ieva Ignatavičienė
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Vytautas Rakauskas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Dace Grauda
- Institute of Biology, University of Latvia, Jelgavas Str. 1, LV-1004 Riga, Latvia;
| | - Petras Prakas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Dalius Butkauskas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| |
Collapse
|
2
|
In Silico Screening and Development of Microsatellite Markers for Genetic Analysis in Perca fluviatilis. Animals (Basel) 2022; 12:ani12141809. [PMID: 35883356 PMCID: PMC9312242 DOI: 10.3390/ani12141809] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
Perca fluviatilis is an economically important species of freshwater fish. To understand the genetic structure of P. fluviatilis in China, 268 samples were collected from Wulungu Lake (WL), Jili Lake (JL), the Wulungu River (WR), and the Kalaeerqisi River (KR). These samples were then analyzed using microsatellite markers. A total of 98,425 microsatellite markers were developed based on the genomic data, and 29 polymorphic microsatellite markers were selected to analyze genetic diversity in this study. The number of alleles (Na) and observed heterozygosity (Ho) per population ranged from 4.621 (KR) to 11.172 (WL) and from 0.510 (KR) to 0.716 (JL), respectively. The results of the polymorphic information content (PIC) showed that the WL, JL, and WR populations were highly polymorphic (PIC≥ 0.5) and that the KR population was moderately polymorphic (0.25 ≤ PIC < 0.5). The genetic differentiation coefficient (Fst) among the four P. fluviatilis populations was 0.074, indicating moderate genetic differentiation among the populations in Xinjiang. The reason for the significant difference between the rivers and lakes could be the presence of a dam blocking the flow of P. fluviatilis. The development of microsatellite markers provides support for population genetics in the future. The evaluation of the genetic structure of P. fluviatilis in Xinjiang provides a reference for the reproduction and conservation of P. fluviatilis.
Collapse
|
3
|
Genetic Diversity and Population Structure of Portunustrituberculatus in Released and Wild Populations Based on Microsatellite DNA Markers from the Yangtze Estuary. DIVERSITY 2022. [DOI: 10.3390/d14050374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Portunus trituberculatus is an important economic species of crab that is artificially bred and released in the Yangtze River Estuary and its adjacent sea areas. Based on six microsatellite markers, we investigate the genetic diversity and structure of 101 P. trituberculatus specimens collected from two hatcheries in Nantong and Zhoushan that participated in stock enhancement in the year 2019. We compared these with 124 wild specimens caught from 13 localities in the estuary. Analysis of several genetic diversity parameters (NA, RS, I, HO, HE, FIS, and FST) for the 15 populations demonstrates that both released and wild populations possess relatively rich genetic diversity. Furthermore, the released groups demonstrate no less genetic variation between themselves than do the wild crabs. Most FIS values are greater than zero, which shows inbreeding is common among specimens with geographically open sites. However, insufficient sampling may have led to a wide distribution of null alleles, a Hardy–Weinberg test disequilibrium in microsatellite markers PN22 and P04, and a lack of crab genetic diversity in site 14. All populations (except locality 14) have not suffered the bottleneck effect. Four subgroups can be seen to roughly spread longitudinally along the sample area by performing pairwise comparisons of genetic distance and FST values among the populations. No obvious topological heterogeneity is discovered among the four subgroups in a phylogenetic tree. The existence of genetic exchange and differentiation among the subgroups is also verified using structure analysis. Therefore, based on this evidence, we propose that the hatchery stock enhancements performed in Nantong and Zhoushan result in no reduction in genetic diversity for wild populations in the Yangtze Estuary in 2019.
Collapse
|
4
|
Kánainé Sipos D, Csenki-Bakos K, Ősz Á, Bokor Z, Kotrik L, Żarski D, Ittzés I, Urbányi B, Kovács B. Twelve new microsatellite loci of Eurasian perch Perca fluviatilis Linnaeus, 1758. Biol Futur 2021; 72:385-393. [PMID: 34554558 DOI: 10.1007/s42977-021-00087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
The Eurasian perch (Perca fluviatilis Linnaeus, 1758) is native to almost entire Eurasia. For over the last two decades, this species became an important candidate for intensive freshwater aquaculture due to its high consumer's acceptance and overall market value. Hence, the intensive production of Eurasian perch has increased considerably allowing effective domestication; there is still a need for the development of effective selective breeding programmes allowing its further expansion. This process, in turn, can be significantly facilitated by molecular genetics. The genetic information of Eurasian perch and its populations is limited. Up to date information of regarding genetic diversity of many populations is still missing, including microsatellites for Eurasian perch, which could be useful during the selective breeding programmes allowing parental assignment and/or to follow heritability of desired traits. In this study, we have developed and characterized new polymorphic microsatellites. Subsequently, those 12 markers have been used further to compare two Hungarian and one Polish Eurasian perch populations. The Hungarian stocks had high genetic similarity (with low diversity), as we assumed, while the Polish population differed significantly. All populations deviated significantly from the Hardy-Weinberg equilibrium, and heterozygote deficiency was detected in all, showing the presence of an anthropogenic effect.
Collapse
Affiliation(s)
- Dóra Kánainé Sipos
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Katalin Csenki-Bakos
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Ágnes Ősz
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Zoltán Bokor
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - László Kotrik
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Daniel Żarski
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - István Ittzés
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary. .,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary.
| |
Collapse
|
5
|
Jaisuk C, Senanan W. Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand. PeerJ 2018; 6:e4487. [PMID: 29568710 PMCID: PMC5845392 DOI: 10.7717/peerj.4487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/20/2018] [Indexed: 11/20/2022] Open
Abstract
Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (n = 30–100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P < 0.05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global FST = 0.022, P < 0.01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized FST (P < 0.05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R2 = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand.
Collapse
Affiliation(s)
- Chaowalee Jaisuk
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand.,Department of Animal Science and Fisheries, Faculty of Science and Agricultural Technology, Rajamangala University of Technology Lanna Nan Campus, Nan, Thailand
| | - Wansuk Senanan
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand
| |
Collapse
|