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Sherzada S, Hussain N, Hussain A, El-Tabakh MAM, Khan SA. Diversity and genetic structure of freshwater shark Wallago attu: an emerging species of commercial interest. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:15571-15579. [PMID: 38300493 DOI: 10.1007/s11356-024-32117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
Pakistan has natural freshwater resources acting as a hotspot for diverse fish fauna. However, this aquatic fauna is declining at an alarming rate due to over-exploitation, habitat degradation, water pollution, climate change, and certain anthropogenic activities. The freshwater shark, Wallago attu, is a popular edible catfish inhabiting these freshwater ecosystems. Habitat degradation, overfishing, and human activities are heavily impacting the natural population of this species. So, sound knowledge about its population structure is necessary for its proper management in natural waters. The current study involves utilizing two mtDNA markers (COI, Cytb) to assess the genetic structure and differentiation among W. attu populations of Pakistani Rivers. Genetic variability analysis indicated a high haplotype (0.343 ± 0.046-0.870 ± 0.023) and low nucleotide diversity (0.0024 ± 0.012-0.0038 ± 0.018) among single and combined gene sequences, respectively. Overall, River Indus was populated with more diverse fauna of Wallago attu as compared to River Chenab and River Ravi. Population pairwise, Fst values (0.40-0.61) were found to be significantly different (p < 0.01) among three Riverine populations based upon combined gene sequences. The gene flow for the combined gene (COI + Cytb) dataset among three populations was less than 1.0. The transition/transversion bias value R (0.58) was calculated for testing of neutral evolution, and it declared low genetic polymorphism among natural riverine populations of Wallago attu. The current study's findings would be meaningful in planning the management and conservation of this economically important catfish in future.
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Affiliation(s)
- Shahid Sherzada
- Department of Zoology, Government College University Lahore, Lahore, Pakistan.
- Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Nimra Hussain
- Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ali Hussain
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | | | - Saeed Akram Khan
- Department of Zoology, Government College University Lahore, Lahore, Pakistan
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin". Nat Commun 2021; 12:2807. [PMID: 33990586 PMCID: PMC8121787 DOI: 10.1038/s41467-021-23096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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Amish SJ, Ali O, Peacock M, Miller M, Robinson M, Smith S, Luikart G, Neville H. Assessing thermal adaptation using family‐based association and
F
ST
outlier tests in a threatened trout species. Mol Ecol 2019; 28:2573-2593. [DOI: 10.1111/mec.15100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Stephen J. Amish
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
| | - Omar Ali
- Department of Animal Science University of California Davis California
| | - Mary Peacock
- Department of Biology University of Nevada Reno Nevada
| | - Michael Miller
- Department of Animal Science University of California Davis California
| | | | - Seth Smith
- Flathead Biological Station University of Montana Polson Montana
| | - Gordon Luikart
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
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Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl 2016; 9:1205-1218. [PMID: 27877200 PMCID: PMC5108213 DOI: 10.1111/eva.12414] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022] Open
Abstract
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | | | - Hans Ellegren
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gordon Luikart
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological StationDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
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Devaux A, Bony S, Plenet S, Sagnes P, Segura S, Suaire R, Novak M, Gilles A, Olivier JM. Field evidence of reproduction impairment through sperm DNA damage in the fish nase (Chondrostoma nasus) in anthropized hydrosystems. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 169:113-122. [PMID: 26523677 DOI: 10.1016/j.aquatox.2015.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/14/2015] [Accepted: 10/17/2015] [Indexed: 06/05/2023]
Abstract
This work aims to explore in the field the relationship between the integrity of sperm DNA and the quality of offspring as a possible cause of the decline of a feral fish population through reproduction impairment. Mature nase (Chondrostoma nasus) were caught during the breeding season in three locations (A-C) of the Rhône River basin and gametes collected by stripping. Sampling locations were chosen according to the following gradient of contamination due to human activities on the watershed: A≤B<C. Samples of a pool of collected oocytes were fertilized with the sperm of individual males and then incubated individually back in the lab to study embryo-larval development as well as using sperm samples to assess DNA integrity. Genetic analysis clearly showed the absence of a difference in genetic structure between the three studied C. nasus populations from the Rhône basin. Sperm DNA integrity was significantly lower in males from station C compared to other ones while sperm biochemical characteristics and fertilization rate remained almost unchanged whatever the station. Mortality and abnormality rates measured at both hatching and at the end of yolk sac resorption stages followed the same trend as the sperm DNA damage, demonstrating an impact of river water quality on nase fitness through a loss of sperm DNA integrity. Since the level of both abnormalities and mortality measured in offspring of fish caught in the most contaminated area reached high values up to 15% and 80%, respectively, the hypothesis that the observed nase decline in Rhône River stemming through selection forces can be put forward.
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Affiliation(s)
- Alain Devaux
- Université de Lyon, USC INRA 1369, UMR CNRS 5023 LEHNA, ENTPE, Rue Maurice Audin, F-69518 Vaulx en Velin, France.
| | - Sylvie Bony
- Université de Lyon, USC INRA 1369, UMR CNRS 5023 LEHNA, ENTPE, Rue Maurice Audin, F-69518 Vaulx en Velin, France
| | - Sandrine Plenet
- Université de Lyon, UMR CNRS 5023 LEHNA, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Pierre Sagnes
- Université de Lyon, UMR CNRS 5023 LEHNA, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Samuel Segura
- Université de Lyon, UMR CNRS 5023 LEHNA, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Rémi Suaire
- Université de Lyon, USC INRA 1369, UMR CNRS 5023 LEHNA, ENTPE, Rue Maurice Audin, F-69518 Vaulx en Velin, France
| | - Morgane Novak
- Université de Lyon, UMR CNRS 5023 LEHNA, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - André Gilles
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Aix Marseille Université, CNRS, IRD, Avignon Université, centre Saint Charles, 3 place Victor Hugo, F-13331 Marseille, France
| | - Jean-Michel Olivier
- Université de Lyon, UMR CNRS 5023 LEHNA, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
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Brodersen J, Seehausen O. Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs. Evol Appl 2014; 7:968-83. [PMID: 25553061 PMCID: PMC4231589 DOI: 10.1111/eva.12215] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/17/2014] [Indexed: 01/10/2023] Open
Abstract
While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys.
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Affiliation(s)
- Jakob Brodersen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and BiogeochemistryKastanienbaum, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and BiogeochemistryKastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of BernBern, Switzerland
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