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Genetic structure and diversity of amphidromous sculpin in Shiretoko, a mountainous peninsula in Japan. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01472-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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2
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Liu S, Wilson JM, Taylor EB, Richards JG. Freshwater adaptation in prickly sculpin (Pisces: Cottidae): intraspecific comparisons reveal evidence for water pH and Na+ concentration driving diversity in gill H+-ATPase and ionoregulation. J Exp Biol 2022; 225:276687. [PMID: 36062522 DOI: 10.1242/jeb.243500] [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: 09/15/2021] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
Phenotypic divergence is a hallmark of adaptive radiation. One example involves differentiation in physiological traits involved in ion regulation among species with contrasting life-styles and living in distinct environments. Differentiation in ion regulation and its ecological implications among populations within species are, however, less well understood. To address this knowledge gap, we collected prickly sculpin (Cottus asper) from distinct habitat types including coastal rivers connected to estuaries, coastal lakes, and interior lakes, all from British Columbia, Canada. We tested for differences in plasma Na+ and Cl-, gill Na+/K+-ATPase and H+-ATPase activities and protein abundance as well as changes in body mass, and arterial blood pH in fish sampled from the field and acclimated to two different freshwater conditions in the laboratory including artificial lake water (ALW) and ion-poor water (IPW). We also tested for associations between environmental water chemistry and the physiological characteristics associated with ion regulation. Transfer to IPW resulted upregulation in gill Na+/K+-ATPase and H+-ATPase activities as well as increases in gill H+-ATPase protein expression level in each habitat compared with the common ALW treatment. Despite the presence of population-within-habitat type differences, significant habitat-type effects were revealed in most of the ion regulation characteristics examined under different acclimation conditions. Significantly lower plasma Cl- was detected in fish from coastal rivers compared to fish from the other two habitat types during the IPW treatment, which was also significantly lower compared with ALW. Similarly, gill Na+/K+-ATPase activity was lower in the coastal river populations in IPW than in fish from coastal and interior lakes, which was not in accordance with the protein expressed in the gill. For gill H+-ATPase, fish from interior lake populations had the highest level of activity across all habitat types under all conditions, which was related to the protein levels in the gill. The activity of gill H+-ATPase was positively correlated with the combined effect of water Na+ and pH under the ALW treatment. Our results suggest that variation in habitat may be an important factor driving differences in gill Na+/K+-ATPase and H+-ATPase activities across populations of C. asper. Further, the combined effect of water Na+ and pH may have played a key role in physiological adaptation in C. asper during post-glacial freshwater colonization and dispersal.
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Affiliation(s)
- Shuang Liu
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Jonathan M Wilson
- Department of Biology, Wilfrid Laurier University, 75 University Ave., Waterloo, ON N2L 3C5, Canada
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
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Young MK, Smith R, Pilgrim KL, Isaak DJ, McKelvey KS, Parkes S, Egge J, Schwartz MK. A Molecular Taxonomy of Cottus in western North America. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Michael K. Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Rebecca Smith
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Kristine L. Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Daniel J. Isaak
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Kevin S. McKelvey
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Sharon Parkes
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Jacob Egge
- Department of Biology, Pacific Lutheran University, Tacoma, WA 98447
| | - Michael K. Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
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Carroll EKT, Vamosi SM. Population genetics of Bull Trout ( Salvelinus confluentus) in the upper Athabasca River basin. Ecol Evol 2021; 11:14509-14520. [PMID: 34765122 PMCID: PMC8571605 DOI: 10.1002/ece3.8110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022] Open
Abstract
Freshwater ecosystems are negatively impacted by a variety of anthropogenic stressors, with concomitant elevated rates of population decline for freshwater aquatic vertebrates. Because reductions in population size and extent can negatively impact genetic diversity and gene flow, which are vital for sustained local adaptation, it is important to measure these characteristics in threatened species that may yet be rescued from extinction. Across its native range, Bull Trout (Salvelinus confluentus) extent and abundance are in decline due to historic overharvest, invasive non-native species, and habitat loss. In Alberta's Eastern Slope region, populations at the range margin have progressively been lost, motivating us to better understand the amount and distribution of genetic variation in headwater habitats and some downstream sites where they continue to persist. Across this region, we sampled 431 Bull Trout from 20 sites in the Athabasca and Saskatchewan River basins and assayed 10 microsatellite loci to characterize within- and among-population genetic variation. The Saskatchewan and Athabasca River basins contained similar levels of heterozygosity but were differentiated from one another. Within the Athabasca River basin, five genetically differentiated clusters were found. Despite the evidence for genetic differentiation, we did not observe significant isolation-by-distance patterns among these sites. Our findings of ample genetic diversity and no evidence for hybridization with non-native Brook Trout in headwater habitats provide motivation to ameliorate downstream habitats and remove anthropogenic barriers to connectivity towards the goal of long-term persistence of this species.
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Affiliation(s)
- Emma K. T. Carroll
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Steven M. Vamosi
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
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Nakajima S, Sueyoshi M, Hirota SK, Ishiyama N, Matsuo A, Suyama Y, Nakamura F. A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity. Heredity (Edinb) 2021; 127:413-422. [PMID: 34417564 PMCID: PMC8478981 DOI: 10.1038/s41437-021-00468-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded insightful results for conservation.
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Affiliation(s)
- Souta Nakajima
- grid.39158.360000 0001 2173 7691Laboratory of Ecosystem Management, Graduate School of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo, Hokkaido Japan
| | - Masanao Sueyoshi
- grid.472015.50000 0000 9513 8387Aqua Restoration Research Center, Public Works Research Institute, KawashimaKasada-machi, Kakamigahara, Gifu Japan
| | - Shun K. Hirota
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Nobuo Ishiyama
- grid.452441.2Forest Research Institute, Hokkaido Research Organization, Koshunai, Bibai, Hokkaido Japan
| | - Ayumi Matsuo
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Yoshihisa Suyama
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Futoshi Nakamura
- grid.39158.360000 0001 2173 7691Laboratory of Ecosystem Management, Graduate School of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo, Hokkaido Japan
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Da Silva MF, Cruz MV, Vidal Júnior JDD, Zucchi MI, Mori GM, De Souza AP. Geographical and environmental contributions to genomic divergence in mangrove forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
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Affiliation(s)
- Michele Fernandes Da Silva
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - João De Deus Vidal Júnior
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (UNESP), São Vicente, SP, Brazil
| | - Anete Pereira De Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Yang M, Xu C, Duchesne P, Ma Q, Yin G, Fang Y, Lu F, Zhang W. Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries. Ecol Evol 2019; 9:3059-3074. [PMID: 30962881 PMCID: PMC6434575 DOI: 10.1002/ece3.4793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/31/2018] [Accepted: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate-high level of genetic differentiation among populations (range F ST: 0.0310-0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none-liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co-contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.
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Affiliation(s)
- Mei Yang
- College of AgricultureYangtze UniversityJingzhouChina
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Chengyuan Xu
- School of Health, Medical and Applied SciencesCentral Queensland UniversityBundabergQueenslandAustralia
| | | | - Qiang Ma
- Shanghai Chongming Dongtan National Nature ReserveShanghaiChina
| | - Ganqiang Yin
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Yang Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Fan Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
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8
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Measuring Genetic Differentiation from Pool-seq Data. Genetics 2018; 210:315-330. [PMID: 30061425 DOI: 10.1534/genetics.118.300900] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/21/2018] [Indexed: 12/26/2022] Open
Abstract
The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of [Formula: see text] for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased [Formula: see text] estimator may question the interpretation of population structure inferred from previous analyses.
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9
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Termignoni-García F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P. Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Mol Ecol 2017; 26:4483-4496. [DOI: 10.1111/mec.14224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/06/2017] [Accepted: 06/12/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Flavia Termignoni-García
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan P. Jaramillo-Correa
- Department of Evolutionary Ecology; Institute of Ecology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan Chablé-Santos
- Department of Zoology; Facultad de Medicina Veterinaria y Zootecnia; Universidad Autónoma de Yucatán; Yucatán México
| | - Mark Liu
- Biodiversity Research Center; Academia Sinica; Taipei Nankang Taiwan
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Patricia Escalante-Pliego
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
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Dennenmoser S, Vamosi SM, Nolte AW, Rogers SM. Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq. Mol Ecol 2016; 26:25-42. [DOI: 10.1111/mec.13805] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Dennenmoser
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Steven M. Vamosi
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Arne W. Nolte
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Institute for Biology; Carl von Ossietzky University Oldenburg; Carl von Ossietzky Str. 9-11 26111 Oldenburg Germany
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
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