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Lee SR, Son DC. Genetic diversity pattern reveals the primary determinant of burcucumber ( Sicyos angulatus L.) invasion in Korea. FRONTIERS IN PLANT SCIENCE 2022; 13:997521. [PMID: 36457533 PMCID: PMC9706109 DOI: 10.3389/fpls.2022.997521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
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Isaak DJ, Young MK, Horan DL, Nagel D, Schwartz MK, McKelvey KS. Do metapopulations and management matter for relict headwater bull trout populations in a warming climate? ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2594. [PMID: 35343015 DOI: 10.1002/eap.2594] [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: 07/11/2021] [Revised: 11/04/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Mountain headwater streams have emerged as important climate refuges for native cold-water species due to their slow climate velocities and extreme physical conditions that inhibit non-native invasions. Species persisting in refuges often do so as fragmented, relict populations from broader historical distributions that are subject to ongoing habitat reductions and increasing isolation as climate change progresses. Key for conservation planning is determining where remaining populations will persist and how habitat restoration strategies can improve biological resilience to enhance the long-term prospects for species of concern. Studying bull trout, a headwater species in the northwestern USA, we developed habitat occupancy models using a data set of population occurrence in 991 natal habitat patches with a suite of novel geospatial covariates derived from high-resolution hydroclimatic scenarios and other sources representing watershed and instream habitat conditions, patch geometry, disturbance, and biological interactions. The best model correctly predicted bull trout occupancy status in 82.6% of the patches and included effects for: patch size estimated as habitat volume, extent of within-patch reaches <9°C mean August temperature, distance to nearest occupied patch, road density, invasive brook trout prevalence, patch slope, and frequency of high winter flows. The model was used to assess 16 scenarios of bull trout occurrence within the study streams that represented a range of restoration strategies under three climatic conditions (baseline, moderate change, and extreme change). Results suggested that regional improvements in bull trout status were difficult to achieve in realistic restoration strategies due to the pervasive nature of climate change and the limited extent of restoration actions given their high costs. However, occurrence probabilities in a subset of patches were highly responsive to restoration actions, suggesting that targeted investments to improve the resilience of some populations may be contextually beneficial. A possible strategy, therefore, is focusing effort on responsive populations near more robust population strongholds, thereby contributing to local enclaves where dispersal among populations further enhances resilience. Equally important, strongholds constituted a small numerical percentage of patches (5%-21%), yet encompassed the large majority of occupied habitat by volume (72%-89%) and their protection could have significant conservation benefits for bull trout.
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Affiliation(s)
- Daniel J Isaak
- Rocky Mountain Research Station, US Forest Service, Boise, Idaho, USA
| | - Michael K Young
- Rocky Mountain Research Station, US Forest Service, Missoula, Montana, USA
| | - Dona L Horan
- Rocky Mountain Research Station, US Forest Service, Boise, Idaho, USA
| | - David Nagel
- Rocky Mountain Research Station, US Forest Service, Boise, Idaho, USA
| | - Michael K Schwartz
- Rocky Mountain Research Station, US Forest Service, Missoula, Montana, USA
| | - Kevin S McKelvey
- Rocky Mountain Research Station, US Forest Service, Missoula, Montana, USA
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Yamazaki D, Ito S, Miura O, Sasaki T, Chiba S. High-throughput SNPs dataset reveal restricted population connectivity of marine gastropod within the narrow distribution range of peripheral oceanic islands. Sci Rep 2022; 12:2119. [PMID: 35136087 PMCID: PMC8825847 DOI: 10.1038/s41598-022-05026-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022] Open
Abstract
Molecular studies based on the high resolution genetic markers help us to grasp the factor shaping the genetic structure of marine organisms. Ecological factors linking to life history traits have often explained the process of genetic structuring in open and connectable oceanic environments. Besides, population genetic divergence can be affected by fragmented habitat, oceanic current, and past geographical events. In the present study, we demonstrated the genetic differentiation of marine gastropod Monodonta sp. within a narrow range of peripheral oceanic islands, the Ogasawara Islands. Genetic analyses were performed not only with a mitochondrial DNA marker but also with a high-throughput SNPs dataset obtained by ddRAD-seq. The results of the mtDNA analyses did not show genetic divergence among populations, while the SNPs dataset detected population genetic differentiation. Population demographic analyses and gene flow estimation suggested that the genetic structure was formed by sea level fluctuation associated with the past climatic change and regulated by temporal oceanographic conditions. These findings provide important insights into population genetic patterns in open and connectable environments.
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Affiliation(s)
- Daishi Yamazaki
- Center for Northeast Asian Studies, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai, Miyagi, 980-8576, Japan.
| | - Shun Ito
- Graduate School of Life Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Tetsuro Sasaki
- Institute of Boninology, Chichijima-Aza-Nishimachi, Ogasawara, Tokyo, 100-2101, Japan
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai, Miyagi, 980-8576, Japan.,Graduate School of Life Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
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Peek RA, O'Rourke SM, Miller MR. Flow modification associated with reduced genetic health of a river‐breeding frog,
Rana boylii. Ecosphere 2021. [DOI: 10.1002/ecs2.3496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis California95616USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis California95616USA
| | - Michael R. Miller
- Department of Animal Science University of California Davis California95616USA
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Camak DT, Osborne MJ, Turner TF. Population genomics and conservation of Gila Trout (Oncorhynchus gilae). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01355-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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8
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River drying influences genetic variation and population structure in an Arctic freshwater fish. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01339-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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King RA, Stockley B, Stevens JR. Small coastal streams-Critical reservoirs of genetic diversity for trout ( Salmo trutta L.) in the face of increasing anthropogenic stressors. Ecol Evol 2020; 10:5651-5669. [PMID: 32607181 PMCID: PMC7319166 DOI: 10.1002/ece3.6306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/05/2022] Open
Abstract
We used microsatellite markers to investigate levels and structuring of genetic diversity in trout (Salmo trutta L.) sampled from 16 rivers along the south coast of Cornwall in southwest England. This region is characterized by many small coastal streams with a few larger catchments. At a regional level, genetic structuring of contemporary populations has been influenced by a combination of events, including the last Ice Age and also more recent human activities over the last millennium. All populations are shown to have gone through strong genetic bottlenecks, coinciding with increased exploitation of mineral resources within catchments, beginning during the Medieval period. At more local levels, contemporary human-induced habitat fragmentation, such as weir and culvert construction, has disproportionally affected trout populations in the smaller catchments within the study area. However, where small catchments are relatively unaffected by such activities, they can host trout populations with diversity levels comparable to those found in larger rivers in the region. We also predict significant future loses of diversity and heterozygosity in the trout populations inhabiting small, isolated catchments. Our study highlights how multiple factors, especially the activity of humans, have and continue to affect the levels and structuring of genetic diversity in trout over long timescales.
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Affiliation(s)
- R. Andrew King
- Department of BiosciencesCollege of Life and Environmental SciencesUniversity of Exeter, Hatherly LaboratoriesExeterUK
| | | | - Jamie R. Stevens
- Department of BiosciencesCollege of Life and Environmental SciencesUniversity of Exeter, Hatherly LaboratoriesExeterUK
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Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01248-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractRed deer (Cervus elaphus) throughout central Europe are influenced by different anthropogenic activities including habitat fragmentation, selective hunting and translocations. This has substantial impacts on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, anthropogenic infrastructures) potentially has led to low levels of genetic diversity. Mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units should be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.
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Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula. Sci Rep 2020; 10:1011. [PMID: 31974505 PMCID: PMC6978382 DOI: 10.1038/s41598-020-57625-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/03/2020] [Indexed: 12/03/2022] Open
Abstract
The modern-day distribution of freshwater fishes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven different rivers to obtain better understand historical gene flow of freshwater fish on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and first colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers flowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the first genetic attempt to confirm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning.
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Jones J, Börger L, Tummers J, Jones P, Lucas M, Kerr J, Kemp P, Bizzi S, Consuegra S, Marcello L, Vowles A, Belletti B, Verspoor E, Van de Bund W, Gough P, Garcia de Leaniz C. A comprehensive assessment of stream fragmentation in Great Britain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 673:756-762. [PMID: 31003103 DOI: 10.1016/j.scitotenv.2019.04.125] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/01/2019] [Accepted: 04/09/2019] [Indexed: 05/25/2023]
Abstract
Artificial barriers are one of the main threats to river ecosystems, resulting in habitat fragmentation and loss of connectivity. Yet, the abundance and distribution of most artificial barriers, excluding high-head dams, is poorly documented. We provide a comprehensive assessment of the distribution and typology of artificial barriers in Great Britain, and estimate for the first time the extent of river fragmentation. To this end, barrier data were compiled from existing databases and were ground-truthed by field surveys in England, Scotland and Wales to derive a correction factor for barrier density across Great Britain. Field surveys indicate that existing barrier databases underestimate barrier density by 68%, particularly in the case of low-head structures (<1 m) which are often missing from current records. Field-corrected barrier density estimates ranged from 0.48 barriers/km in Scotland to 0.63 barriers/km in Wales, and 0.75 barriers/km in England. Corresponding estimates of stream fragmentation by weirs and dams only, measured as mean barrier-free length, were 12.30 km in Scotland, 6.68 km in Wales and 5.29 km in England, suggesting the extent of river modification differs between regions. Our study indicates that 97% of the river network in Great Britain is fragmented and <1% of the catchments are free of artificial barriers.
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Affiliation(s)
- Joshua Jones
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Luca Börger
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK
| | - Jeroen Tummers
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Peter Jones
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK
| | - Martyn Lucas
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Jim Kerr
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Paul Kemp
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Simone Bizzi
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK
| | - Lucio Marcello
- Rivers and Lochs Institute, University of Highlands and Islands, Inverness, UK
| | - Andrew Vowles
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Barbara Belletti
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milano, Italy
| | - Eric Verspoor
- Rivers and Lochs Institute, University of Highlands and Islands, Inverness, UK
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Pregler KC, Kanno Y, Rankin D, Coombs JA, Whiteley AR. Characterizing genetic integrity of rear-edge trout populations in the southern Appalachians. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1116-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Euclide P, Marsden JE. Role of drainage and barriers in the genetic structuring of a tessellated darter population. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1107-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish. Heredity (Edinb) 2018; 120:515-532. [PMID: 29326479 PMCID: PMC5943333 DOI: 10.1038/s41437-017-0008-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022] Open
Abstract
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (FST = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.
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Robinson ZL, Coombs JA, Hudy M, Nislow KH, Letcher BH, Whiteley AR. Experimental test of genetic rescue in isolated populations of brook trout. Mol Ecol 2017; 26:4418-4433. [PMID: 28664980 DOI: 10.1111/mec.14225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/21/2017] [Accepted: 06/05/2017] [Indexed: 12/27/2022]
Abstract
Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.
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Affiliation(s)
- Zachary L Robinson
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Jason A Coombs
- U.S. Forest Service, Northern Research Station, University of Massachusetts, Amherst, MA, USA
| | | | - Keith H Nislow
- U.S. Forest Service, Northern Research Station, University of Massachusetts, Amherst, MA, USA
| | - Benjamin H Letcher
- U.S. Geological Survey, Leetown Science Center, S.O. Conte Anadromous Fish Research Center, Turners Falls, MA, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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Prentice MB, Bowman J, Khidas K, Koen EL, Row JR, Murray DL, Wilson PJ. Selection and drift influence genetic differentiation of insular Canada lynx ( Lynx canadensis) on Newfoundland and Cape Breton Island. Ecol Evol 2017; 7:3281-3294. [PMID: 28480025 PMCID: PMC5415520 DOI: 10.1002/ece3.2945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/27/2017] [Accepted: 03/05/2017] [Indexed: 01/16/2023] Open
Abstract
Island populations have long been important for understanding the dynamics and mechanisms of evolution in natural systems. While genetic drift is often strong on islands due to founder events and population bottlenecks, the strength of selection can also be strong enough to counteract the effects of drift. Here, we used several analyses to identify the roles of genetic drift and selection on genetic differentiation and diversity of Canada lynx (Lynx canadensis) across eastern Canada, including the islands of Cape Breton and Newfoundland. Specifically, we assessed whether we could identify a genetic component to the observed morphological differentiation that has been reported across insular and mainland lynx. We used a dinucleotide repeat within the promoter region of a functional gene that has been linked to mammalian body size, insulin-like growth factor-1 (IGF-1). We found high genetic differentiation at neutral molecular markers but convergence of allele frequencies at the IGF-1 locus. Thus, we showed that while genetic drift has influenced the observed genetic structure of lynx at neutral molecular markers, natural selection has also played a role in the observed patterns of genetic diversity at the IGF-1 locus of insular lynx.
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Affiliation(s)
- Melanie B Prentice
- Department of Environmental and Life Sciences Trent University Peterborough ON Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Peterborough ON Canada
| | - Kamal Khidas
- Vertebrate Zoology Canadian Museum of Nature Ottawa ON Canada
| | - Erin L Koen
- Biology Department Trent University Peterborough ON Canada
| | - Jeffrey R Row
- Department of Environment and Resource Studies University of Waterloo Waterloo ON Canada
| | | | - Paul J Wilson
- Biology Department Trent University Peterborough ON Canada
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Carim K, Vindenes Y, Eby L, Barfoot C, Vøllestad L. Life history, population viability, and the potential for local adaptation in isolated trout populations. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Whiteley AR, Coombs JA, O'Donnell MJ, Nislow KH, Letcher BH. Keeping things local: Subpopulation Nb and Ne in a stream network with partial barriers to fish migration. Evol Appl 2017; 10:348-365. [PMID: 28352295 PMCID: PMC5367083 DOI: 10.1111/eva.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/11/2016] [Indexed: 01/17/2023] Open
Abstract
For organisms with overlapping generations that occur in metapopulations, uncertainty remains regarding the spatiotemporal scale of inference of estimates of the effective number of breeders (N^b) and whether these estimates can be used to predict generational Ne. We conducted a series of tests of the spatiotemporal scale of inference of estimates of Nb in nine consecutive cohorts within a long‐term study of brook trout (Salvelinus fontinalis). We also tested a recently developed approach to estimate generational Ne from N^b and compared this to an alternative approach for estimating N^e that also accounts for age structure. Multiple lines of evidence were consistent with N^b corresponding to the local (subpopulation) spatial scale and the cohort‐specific temporal scale. We found that at least four consecutive cohort‐specific estimates of N^b were necessary to obtain reliable estimates of harmonic mean N^b for a subpopulation. Generational N^e derived from cohort‐specific N^b was within 7%–50% of an alternative approach to obtain N^e, suggesting some population specificity for concordance between approaches. Our results regarding the spatiotemporal scale of inference for Nb should apply broadly to many taxa that exhibit overlapping generations and metapopulation structure and point to promising avenues for using cohort‐specific N^b for local‐scale genetic monitoring.
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Affiliation(s)
- Andrew R Whiteley
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences College of Forestry and Conservation University of Montana Missoula MT USA
| | - Jason A Coombs
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA; U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA USA
| | - Matthew J O'Donnell
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA USA
| | - Keith H Nislow
- U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA USA
| | - Benjamin H Letcher
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA USA
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Vergilino R, Leung C, Angers B. Inconsistent phylogeographic pattern between a sperm dependent fish and its host: in situ hybridization vs dispersal. BMC Evol Biol 2016; 16:183. [PMID: 27600616 PMCID: PMC5012089 DOI: 10.1186/s12862-016-0754-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 08/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background Co-dispersal of sperm-dependent hybrids and their sexual relatives is expected to result in consistent spatial patterns between assemblages of hybrids and genetic structure of parental species. However, local hybridization events may blur this signal as assemblages could be organized under different connectivity constraints. This study aims at testing the hypothesis of local hybridization events by comparing the assemblage of hybrid fish Chrosomus eos-neogaeus to the genetic diversity of one of its parental species, Chrosomus eos. Results An extensive survey performed on a total of 132 sites located in two regions of Southern Quebec (West-Qc and East-Qc) revealed a distinct organization of hybrid lineages. One of the six hybrid lineages detected in West-Qc is widespread throughout this region resulting in a low α-diversity (1.38) and β-diversity (4.35). On the other hand, 36 hybrid lineages were detected in East-Qc and displayed narrow geographic distributions leading to a high α-diversity (2.30) and β-diversity (15.68). In addition, the C. eos multilocus haplotype of several of these hybrids is assigned to their respective sympatric C. eos population. Finally, contrasting with hybrids, the paternal species C. eos displayed a higher ρST in West-Qc (0.2300) than in East-Qc (0.0734). Conclusion The unusually high diversity of hybrid lineages in East-Qc as well as the spatial organization and the close genetic relationship with C. eos sympatric populations support the hypothesis that multiple hybridization events occurred in situ. These findings coupled to the near absence of the maternal species Chrosomus neogeaus suggest that the decline of this species could be the trigger event at the origin of the high rates of spontaneous hybridization in this region. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0754-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roland Vergilino
- Department of biological sciences, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Christelle Leung
- Department of biological sciences, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Bernard Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada.
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Ridley CE, Alexander LC. Applying gene flow science to environmental policy needs: a boundary work perspective. Evol Appl 2016; 9:924-36. [PMID: 27468309 PMCID: PMC4947153 DOI: 10.1111/eva.12393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 05/09/2016] [Indexed: 11/27/2022] Open
Abstract
One application of gene flow science is the policy arena. In this article, we describe two examples in which the topic of gene flow has entered into the U.S. national environmental policymaking process: regulation of genetically engineered crops and clarification of the jurisdictional scope of the Clean Water Act. We summarize both current scientific understanding and the legal context within which gene flow science has relevance. We also discuss the process by which scientific knowledge has been synthesized and communicated to decision-makers in these two contexts utilizing the concept of 'boundary work'. Boundary organizations, the work they engage in to bridge the worlds of science, policy, and practice, and the boundary objects they produce to translate scientific knowledge existed in both examples. However, the specific activities and attributes of the objects produced varied based on the needs of the decision-makers. We close with suggestions for how scientists can contribute to or engage in boundary work with policymakers.
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Affiliation(s)
- Caroline E. Ridley
- National Center for Environmental AssessmentU.S. Environmental Protection Agency, Office of Research and DevelopmentWashingtonDCUSA
| | - Laurie C. Alexander
- National Center for Environmental AssessmentU.S. Environmental Protection Agency, Office of Research and DevelopmentWashingtonDCUSA
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22
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Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0867-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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FUNK WCHRIS, LOVICH ROBERTE, HOHENLOHE PAULA, HOFMAN COURTNEYA, MORRISON SCOTTA, SILLETT TSCOTT, GHALAMBOR CAMERONK, MALDONADO JESUSE, RICK TORBENC, DAY MITCHD, POLATO NICHOLASR, FITZPATRICK SARAHW, COONAN TIMOTHYJ, CROOKS KEVINR, DILLON ADAM, GARCELON DAVIDK, KING JULIEL, BOSER CHRISTINAL, GOULD NICHOLAS, ANDELT WILLIAMF. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol 2016; 25:2176-94. [PMID: 26992010 PMCID: PMC4877267 DOI: 10.1111/mec.13605] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 01/02/2023]
Abstract
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
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Affiliation(s)
- W. CHRIS FUNK
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - ROBERT E. LOVICH
- Naval Facilities Engineering Command Southwest, 1220 Pacific Highway, San Diego, CA 92132, USA
| | - PAUL A. HOHENLOHE
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - COURTNEY A. HOFMAN
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | | | - T. SCOTT SILLETT
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013-7012, USA
| | - CAMERON K. GHALAMBOR
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - JESUS E. MALDONADO
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - TORBEN C. RICK
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - MITCH D. DAY
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - NICHOLAS R. POLATO
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - SARAH W. FITZPATRICK
- Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - TIMOTHY J. COONAN
- National Park Service, Channel Islands National Park, 1901 Spinnaker Drive, Ventura, CA 93001, USA
| | - KEVIN R. CROOKS
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
| | - ADAM DILLON
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
| | - DAVID K. GARCELON
- Institute for Wildlife Studies, P.O. Box 1104, Arcata, CA 95518, USA
| | - JULIE L. KING
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | | | - NICHOLAS GOULD
- Fisheries, Wildlife, and Conservation Biology, North Carolina State University, Turner House, Box 7646, Raleigh, NC 27695-7646, USA
| | - WILLIAM F. ANDELT
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
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Slow climate velocities of mountain streams portend their role as refugia for cold-water biodiversity. Proc Natl Acad Sci U S A 2016; 113:4374-9. [PMID: 27044091 DOI: 10.1073/pnas.1522429113] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The imminent demise of montane species is a recurrent theme in the climate change literature, particularly for aquatic species that are constrained to networks and elevational rather than latitudinal retreat as temperatures increase. Predictions of widespread species losses, however, have yet to be fulfilled despite decades of climate change, suggesting that trends are much weaker than anticipated and may be too subtle for detection given the widespread use of sparse water temperature datasets or imprecise surrogates like elevation and air temperature. Through application of large water-temperature databases evaluated for sensitivity to historical air-temperature variability and computationally interpolated to provide high-resolution thermal habitat information for a 222,000-km network, we estimate a less dire thermal plight for cold-water species within mountains of the northwestern United States. Stream warming rates and climate velocities were both relatively low for 1968-2011 (average warming rate = 0.101 °C/decade; median velocity = 1.07 km/decade) when air temperatures warmed at 0.21 °C/decade. Many cold-water vertebrate species occurred in a subset of the network characterized by low climate velocities, and three native species of conservation concern occurred in extremely cold, slow velocity environments (0.33-0.48 km/decade). Examination of aggressive warming scenarios indicated that although network climate velocities could increase, they remain low in headwaters because of strong local temperature gradients associated with topographic controls. Better information about changing hydrology and disturbance regimes is needed to complement these results, but rather than being climatic cul-de-sacs, many mountain streams appear poised to be redoubts for cold-water biodiversity this century.
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Kavembe GD, Kautt AF, Machado-Schiaffino G, Meyer A. Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa. Mol Ecol 2016; 25:1610-25. [DOI: 10.1111/mec.13461] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Geraldine D. Kavembe
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- Department of Biology; School of Pure and Applied Sciences; South Eastern Kenya University; P. O. Box 170 90200 Kitui Kenya
| | - Andreas F. Kautt
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- International Max Planck Research School for Organismal Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Gonzalo Machado-Schiaffino
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- International Max Planck Research School for Organismal Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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Shikano T, Järvinen A, Marjamäki P, Kahilainen KK, Merilä J. Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia. PLoS One 2015; 10:e0140344. [PMID: 26468642 PMCID: PMC4607410 DOI: 10.1371/journal.pone.0140344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/24/2015] [Indexed: 01/01/2023] Open
Abstract
Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean FST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (Ne) ranged from seven to 228 and were significantly correlated with those of historical Ne but not with lake size. A census size (NC) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest Ne (i.e. Ne/NC = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.
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Affiliation(s)
- Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Antero Järvinen
- Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, Finland
| | - Paula Marjamäki
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Kimmo K. Kahilainen
- Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, Finland
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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Robin VV, Gupta P, Thatte P, Ramakrishnan U. Islands within islands: two montane palaeo-endemic birds impacted by recent anthropogenic fragmentation. Mol Ecol 2015; 24:3572-84. [DOI: 10.1111/mec.13266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/29/2022]
Affiliation(s)
- V. V. Robin
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
| | - Pooja Gupta
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
| | - Prachi Thatte
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
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Yan W, Hou B, Xue Q, Geng L, Ding X. Different evolutionary processes in shaping the genetic composition of Dendrobium nobile in southwest China. Genetica 2015; 143:361-71. [PMID: 25838240 DOI: 10.1007/s10709-015-9835-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/25/2015] [Indexed: 11/25/2022]
Abstract
Knowledge of population genetic structure and intrapopulation genetic variation is important for understanding population dynamics and evolutionary processes. Dendrobium nobile is an endangered traditional Chinese tonic medicine. In order to analyze the population differentiation and genetic diversity in D. nobile and propose proper conservation measurements, we genotyped 102 individual plants from 7 natural populations distributed across southwest China at 9 microsatellite loci. Seven pairs of genomic SSR primers were newly designed, and two pairs were chosen from the EST-SSRs. According to the results, the genetic process of D. nobile on Hainan Island and the Chinese mainland might be affected by different evolutionary processes, the genetic drift caused by founder effect has played an important role in shaping the genetic constitution of the Island population. The population of D. nobile in Hainan Island was highly differentiated and displayed low levels of genetic diversity. For the conservation management plans of D. nobile, we propose that individuals in Hainan Island with rare alleles need to be conserved with top priority, and those individuals with rare alleles and the most common alleles also should be concerned. The seven new microsatellite loci may be informative for further evaluation and conservation of the genetic diversity of D. nobile.
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Affiliation(s)
- Wenjin Yan
- College of Life Sciences, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210046, China
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Sandlund OT, Karlsson S, Thorstad EB, Berg OK, Kent MP, Norum ICJ, Hindar K. Spatial and temporal genetic structure of a river-resident Atlantic salmon (Salmo salar) after millennia of isolation. Ecol Evol 2014; 4:1538-54. [PMID: 24967074 PMCID: PMC4063457 DOI: 10.1002/ece3.1040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 01/18/2023] Open
Abstract
The river-resident Salmo salar ("småblank") has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (F ST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size Ne of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005-2008) compared with historical samples (1955-56 and 1978-79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta-population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important.
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Affiliation(s)
- Odd Terje Sandlund
- Norwegian Institute for Nature Research (NINA) PO Box 5685, No-7485, Trondheim, Norway
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA) PO Box 5685, No-7485, Trondheim, Norway
| | - Eva B Thorstad
- Norwegian Institute for Nature Research (NINA) PO Box 5685, No-7485, Trondheim, Norway
| | - Ole Kristian Berg
- Department of Biology, Norwegian University of Science and Technology (NTNU) No-7491, Trondheim, Norway
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences (IHA), Center for Integrative Genetics (CIGENE), Norwegian University of Life Sciences PO Box 5003, No-1432, Ås, Norway
| | - Ine C J Norum
- Department of Biology, Norwegian University of Science and Technology (NTNU) No-7491, Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA) PO Box 5685, No-7485, Trondheim, Norway
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Bond MH, Crane PA, Larson WA, Quinn TP. Is isolation by adaptation driving genetic divergence among proximate Dolly Varden char populations? Ecol Evol 2014; 4:2515-32. [PMID: 25360283 PMCID: PMC4203295 DOI: 10.1002/ece3.1113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/16/2014] [Accepted: 04/23/2014] [Indexed: 01/26/2023] Open
Abstract
Numerous studies of population genetics in salmonids and other anadromous fishes have revealed that population structure is generally organized into geographic hierarchies (isolation by distance), but significant structure can exist in proximate populations due to varying selective pressures (isolation by adaptation). In Chignik Lakes, Alaska, anadromous Dolly Varden char (Salvelinus malma) spawn in nearly all accessible streams throughout the watershed, including those draining directly to an estuary, Chignik Lagoon, into larger rivers, and into lakes. Collections of Dolly Varden fry from 13 streams throughout the system revealed low levels of population structure among streams emptying into freshwater. However, much stronger genetic differentiation was detected between streams emptying into freshwater and streams flowing directly into estuarine environments. This fine-scale reproductive isolation without any physical barriers to migration is likely driven by differences in selection pressures across freshwater and estuarine environments. Estuary tributaries had fewer larger, older juveniles, suggesting an alternative life history of smolting and migration to the marine environment at a much smaller size than occurs in the other populations. Therefore, genetic data were consistent with a scenario where isolation by adaptation occurs between populations of Dolly Varden in the study system, and ecological data suggest that this isolation may partially be a result of a novel Dolly Varden life history of seawater tolerance at a smaller size than previously recognized.
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Affiliation(s)
- Morgan H Bond
- School of Aquatic and Fishery Sciences, University of Washington Box 355020, Seattle, Washington, 98195
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service 1011 East Tudor Road, Anchorage, Alaska, 99503
| | - Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington Box 355020, Seattle, Washington, 98195
| | - Tom P Quinn
- School of Aquatic and Fishery Sciences, University of Washington Box 355020, Seattle, Washington, 98195
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Yuan N, Sun Y, Comes HP, Fu CX, Qiu YX. Understanding population structure and historical demography in a conservation context: population genetics of the endangered Kirengeshoma palmata (Hydrangeaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:521-529. [PMID: 24650862 DOI: 10.3732/ajb.1400043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Both historical and contemporary microevolutionary processes greatly influence the genetic patterns of East Asian plant endemics, but the spatial and temporal contexts of these processes remain poorly understood. Here, we investigate the relative influences of historical and contemporary gene flow and drift on the population genetic structure of Kirengeshoma palmata, a perennial herb from East China and South Japan. METHODS We used data from nine polymorphic microsatellite loci to assess the levels of genetic diversity, effective population size, and contemporary and historical gene flow for six of the seven known populations. KEY RESULTS We found high levels of inbreeding and allelic diversity within populations. Both contemporary and historical migration rates among populations were low, and a test of alternate models of population history strongly favored a model of long-term drift-migration equilibrium. We inferred declines in population size ca. 10,000-100,000 yr ago, but failed to detect recent declines. Bayesian clustering divided K. palmata populations into three genetic clusters, two of which were consistent with a glacial refugium hypothesis for two mountain ranges in East China. CONCLUSIONS These results suggest that anthropogenic fragmentation has had little effect on the genetic characteristics of Chinese K. palmata. Rather, past decline in population size due to Late Pleistocene climate change as well as restricted pollen and seed dispersal may have contributed to low levels of both historical and contemporary gene flow, resulting in high genetic differentiation between adjacent mountain ranges due to genetic drift and inbreeding.
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Affiliation(s)
- Na Yuan
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Musilová Z, Kalous L, Petrtýl M, Chaloupková P. Cichlid fishes in the Angolan headwaters region: molecular evidence of the ichthyofaunal contact between the Cuanza and Okavango-Zambezi systems. PLoS One 2013; 8:e65047. [PMID: 23724120 PMCID: PMC3664563 DOI: 10.1371/journal.pone.0065047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 04/25/2013] [Indexed: 12/03/2022] Open
Abstract
The headwaters of five large African river basins flow through the Bié Plateau in Angola and still remain faunistically largely unexplored. We investigated fish fauna from the Cuanza and Okavango-Zambezi river systems from central Angola. We reconstructed molecular phylogenies of the most common cichlid species from the region, Tilapia sparrmanii and Serranochromis macrocephalus, using both mitochondrial and nuclear markers. We found evidence for ichthyofaunal contact and gene flow between the Cuanza and Okavango-Zambezi watersheds in the Bié Plateau in central Angola. Waterfalls and rapids also appeared to restrict genetic exchange among populations within the Cuanza basin. Further, we found that the Angolan Serranochromis cichlid fishes represent a monophyletic lineage with respect to other haplochromines, including the serranochromines from the Congo and Zambezi rivers. This study represents an important initial step in a biodiversity survey of this extremely poorly explored region, as well as giving further understanding to species distributions and gene flow both between and within river basins.
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Affiliation(s)
- Zuzana Musilová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics AV ČR v.v.i, Liběchov, Czech Republic.
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Natural and anthropogenic drivers of genetic structure and low genetic variation in the endangered freshwater cod, Maccullochella mariensis. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0490-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Thaulow J, Borgstrøm R, Heun M. Brown trout population structure highly affected by multiple stocking and river diversion in a high mountain national park. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0438-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Harris LN, Howland KL, Kowalchuk MW, Bajno R, Lindsay MM, Taylor EB. Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems. Ecol Evol 2012; 3:145-61. [PMID: 23404390 PMCID: PMC3568850 DOI: 10.1002/ece3.439] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/22/2012] [Accepted: 10/29/2012] [Indexed: 11/17/2022] Open
Abstract
Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.
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Affiliation(s)
- Les N Harris
- Fisheries and Oceans Canada 501 University Crescent, Winnipeg, MB, Canada, R3T 2N6
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Hare MP, Nunney L, Schwartz MK, Ruzzante DE, Burford M, Waples RS, Ruegg K, Palstra F. Understanding and estimating effective population size for practical application in marine species management. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:438-449. [PMID: 21284731 DOI: 10.1111/j.1523-1739.2010.01637.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Effective population size (N(e)) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N(e) is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, N(e) has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved N(e) estimation; however, some obstacles remain for the practical application of N(e) estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of N(e) over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary N(e) estimates and suggest that different sampling designs can be combined to compare largely independent measures of N(e) for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary N(e) and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating N(e) by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating N(e) estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in N(e) from hatchery-based population supplementation.
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Affiliation(s)
- Matthew P Hare
- Department of Natural Resources, Cornell University, Ithaca NY 14853, USA.
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