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Aitken SN, Jordan R, Tumas HR. Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:707-736. [PMID: 38594931 DOI: 10.1146/annurev-arplant-070523-044239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.
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Affiliation(s)
- Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| | | | - Hayley R Tumas
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
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2
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Cavill EL, Morales HE, Sun X, Westbury MV, van Oosterhout C, Accouche W, Zora A, Schulze MJ, Shah N, Adam P, Brooke MDL, Sweet P, Gopalakrishnan S, Gilbert MTP. When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evol Appl 2024; 17:e13739. [PMID: 38948538 PMCID: PMC11212007 DOI: 10.1111/eva.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.
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Affiliation(s)
- Emily L. Cavill
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Xin Sun
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | | | - Anna Zora
- Fregate Island Sanctuary LtdVictoriaSeychelles
| | | | | | | | | | - Paul Sweet
- American Museum of Natural HistoryNew YorkUSA
| | | | - M. Thomas P. Gilbert
- The Globe Institute, University of CopenhagenCopenhagenDenmark
- University Museum, Norwegian University of Science and TechnologyTrondheimNorway
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3
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Nordstrom SW, Hufbauer RA, Olazcuaga L, Durkee LF, Melbourne BA. How density dependence, genetic erosion and the extinction vortex impact evolutionary rescue. Proc Biol Sci 2023; 290:20231228. [PMID: 37989246 PMCID: PMC10688442 DOI: 10.1098/rspb.2023.1228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity and the fixation of maladaptive alleles, hindered adaptation and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.
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Affiliation(s)
- Scott W. Nordstrom
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Ruth A. Hufbauer
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Laure Olazcuaga
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Lily F. Durkee
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Brett A. Melbourne
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
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4
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Black JG, van Rooyen ARJ, Heinze D, Gaffney R, Hoffmann AA, Schmidt TL, Weeks AR. Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii). Mol Ecol 2023. [PMID: 38013623 DOI: 10.1111/mec.17224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Identifying and analysing isolated populations is critical for conservation. Isolation can make populations vulnerable to local extinction due to increased genetic drift and inbreeding, both of which should leave imprints of decreased genome-wide heterozygosity. While decreases in heterozygosity among populations are frequently investigated, fewer studies have analysed how heterozygosity varies among individuals, including whether heterozygosity varies geographically along lines of discrete population structure or with continuous patterns analogous to isolation by distance. Here we explore geographical patterns of differentiation and individual heterozygosity in the threatened eastern barred bandicoot (Perameles gunnii) in Tasmania, Australia, using genomic data from 85 samples collected between 2008 and 2011. Our analyses identified two isolated demes undergoing significant genetic drift, and several areas of fine-scale differentiation across Tasmania. We observed discrete genetic structures across geographical barriers and continuous patterns of isolation by distance, with little evidence of recent or historical migration. Using a recently developed analytical pipeline for estimating autosomal heterozygosity, we found individual heterozygosities varied within demes by up to a factor of two, and demes with low-heterozygosity individuals also still contained those with high heterozygosity. Spatial interpolation of heterozygosity scores clarified these patterns and identified the isolated Tasman Peninsula as a location where low-heterozygosity individuals were more common than elsewhere. Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualised metric for identifying source animals for translocation.
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Affiliation(s)
- John G Black
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Dean Heinze
- Research Centre of Applied Alpine Ecology, La Trobe University, Melbourne, Victoria, Australia
| | - Robbie Gaffney
- Department of Natural Resources and Environment, Hobart, Tasmania, Australia
| | - Ary A Hoffmann
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas L Schmidt
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew R Weeks
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
- Cesar Australia, Brunswick, Victoria, Australia
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5
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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6
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Santos IGD, Verzegnazzi AL, Edwards J, Frei UK, Boerman N, Tonello Zuffo L, Pires LPM, de La Fuente G, Lübberstedt T. Usefulness of temperate-adapted maize lines developed by doubled haploid and single-seed descent methods. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1829-1841. [PMID: 35305125 DOI: 10.1007/s00122-022-04075-2] [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: 08/09/2021] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Spontaneous haploid genome doubling is not associated with undesirable linkage drag effects. The presence of spontaneous doubling genes allows maximum exploitation of variability from the temperate-adapted BS39 population Tropical non-elite maize (Zea mays L.) germplasm, such as BS39, provides a unique opportunity for broadening the genetic base of U.S. Corn Belt germplasm. In vivo doubled haploid (DH) technology has been used to efficiently exploit non-elite germplasm. It can help to purge deleterious recessive alleles. The objectives of this study were to determine the usefulness of BS39-derived inbred lines using both SSD and DH methods, to determine the impact of spontaneous as compared with artificial haploid genome doubling on genetic variance among BS39-derived DH lines, and to identify SNP markers associated with agronomic traits among BS39 inbreds monitored at testcross level. We developed two sets of inbred lines directly from BS39 by DH and SSD methods, named BS39_DH and BS39_SSD. Additionally, two sets were derived from a cross between BS39 and A427 (SHGD donor) by DH and SSD methods, named BS39 × A427_DH and BS39 × A427_SSD, respectively. Grain yield, moisture, plant height, ear height, stalk lodging, and root lodging were measured to estimate genetic parameters. For genome-wide association analysis, inbred lines were genotyped using genotype-by-sequencing and Diversity Array Technology Sequencing (DArTSeq). Some BS39-derived inbred lines performed better than elite germplasm inbreds and all sets showed significant genetic variance. The presence of spontaneous haploid genome doubling genes did not affect performance of inbred lines. Five SNPs were significant and three of them located within genes related to plant development or abiotic stresses. These results demonstrate the potential of BS39 to add novel alleles to temperate elite germplasm.
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Affiliation(s)
| | | | - Jode Edwards
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - Ursula K Frei
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Nicholas Boerman
- USDA-ARS, Southern Plains Range Research Station, Woodward, OK, USA
| | - Leandro Tonello Zuffo
- Department of Plant Sciences, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
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7
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Chang SL, Ward HGM, Elliott LD, Russello MA. Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon. Sci Rep 2022; 12:3441. [PMID: 35236892 PMCID: PMC8891347 DOI: 10.1038/s41598-022-07309-x] [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: 12/31/2021] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or “hybrid”. Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan® assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2 backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~ 74% of which were B2 backcross or F2. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.
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Affiliation(s)
- Sarah L Chang
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Hillary G M Ward
- Lands and Natural Resource Operations and Rural Development, British Columbia Ministry of Forests, Penticton, BC, Canada
| | - Lucas D Elliott
- Department of Biology, University of British Columbia, Kelowna, BC, Canada.,UiT The Arctic University of Norway, Tromsø, Norway
| | - Michael A Russello
- Department of Biology, University of British Columbia, Kelowna, BC, Canada.
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8
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Adams PE, Crist AB, Young EM, Willis JH, Phillips PC, Fierst JL. Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations. Mol Biol Evol 2022; 39:msab330. [PMID: 34791426 PMCID: PMC8789292 DOI: 10.1093/molbev/msab330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Haploid organisms and selfing organisms like the nematode Caenorhabditis elegans are capable of rapid recovery from the fixation of novel deleterious mutation; however, the potential for recovery and genomic consequences of inbreeding in diploid, outcrossing organisms are not well understood. We sought to answer two questions: 1) Can a diploid, outcrossing population recover from inbreeding via standing genetic variation and new mutation? and 2) How does allelic diversity change during recovery? We inbred C. remanei, an outcrossing relative of C. elegans, through brother-sister mating for 30 generations followed by recovery at large population size. Inbreeding reduced fitness but, surprisingly, recovery from inbreeding at large populations sizes generated only very moderate fitness recovery after 300 generations. We found that 65% of ancestral single nucleotide polymorphisms (SNPs) were fixed in the inbred population, far fewer than the theoretical expectation of ∼99%. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous, and reproductive systems changed reproducibly across replicates, indicating that strong selection for fitness recovery does exist. Our results indicate that recovery from inbreeding depression via standing genetic variation and mutation is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for recovery of small populations.
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Affiliation(s)
- Paula E Adams
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Anna B Crist
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Ellen M Young
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Janna L Fierst
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
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Miao J, Farhat P, Wang W, Ruhsam M, Milne R, Yang H, Tso S, Li J, Xu J, Opgenoorth L, Miehe G, Mao K. Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau. ANNALS OF BOTANY 2021; 128:903-918. [PMID: 34472580 PMCID: PMC8577208 DOI: 10.1093/aob/mcab114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). METHODS The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species. KEY RESULTS Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter. CONCLUSIONS This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.
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Affiliation(s)
- Jibin Miao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Perla Farhat
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Wentao Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Richard Milne
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jingjing Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lars Opgenoorth
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Georg Miehe
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
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10
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Olazcuaga L, Foucaud J, Gautier M, Deschamps C, Loiseau A, Leménager N, Facon B, Ravigné V, Hufbauer RA, Estoup A, Rode NO. Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments. J Evol Biol 2021; 34:1225-1240. [PMID: 34097795 PMCID: PMC8457093 DOI: 10.1111/jeb.13878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/23/2021] [Accepted: 05/31/2021] [Indexed: 01/09/2023]
Abstract
The process of local adaptation involves differential changes in fitness over time across different environments. Although experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analysed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii.
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Affiliation(s)
- Laure Olazcuaga
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France.,Department of Agricultural Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Julien Foucaud
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Candice Deschamps
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Nicolas Leménager
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Benoit Facon
- INRAE, UMR Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, La Réunion, France
| | | | - Ruth A Hufbauer
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France.,Department of Agricultural Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Arnaud Estoup
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Nicolas O Rode
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
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11
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Pointer MD, Gage MJG, Spurgin LG. Tribolium beetles as a model system in evolution and ecology. Heredity (Edinb) 2021; 126:869-883. [PMID: 33767370 PMCID: PMC8178323 DOI: 10.1038/s41437-021-00420-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023] Open
Abstract
Flour beetles of the genus Tribolium have been utilised as informative study systems for over a century and contributed to major advances across many fields. This review serves to highlight the significant historical contribution that Tribolium study systems have made to the fields of ecology and evolution, and to promote their use as contemporary research models. We review the broad range of studies employing Tribolium to make significant advances in ecology and evolution. We show that research using Tribolium beetles has contributed a substantial amount to evolutionary and ecological understanding, especially in the fields of population dynamics, reproduction and sexual selection, population and quantitative genetics, and behaviour, physiology and life history. We propose a number of future research opportunities using Tribolium, with particular focus on how their amenability to forward and reverse genetic manipulation may provide a valuable complement to other insect models.
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Affiliation(s)
- Michael D Pointer
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Matthew J G Gage
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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12
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Jones MR, Mills LS, Jensen JD, Good JM. The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares. Am Nat 2020; 196:316-332. [DOI: 10.1086/710022] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Svensson EI, Connallon T. How frequency-dependent selection affects population fitness, maladaptation and evolutionary rescue. Evol Appl 2019; 12:1243-1258. [PMID: 31417612 PMCID: PMC6691226 DOI: 10.1111/eva.12714] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/31/2018] [Accepted: 09/12/2018] [Indexed: 01/04/2023] Open
Abstract
Frequency-dependent (FD) selection is a central process maintaining genetic variation and mediating evolution of population fitness. FD selection has attracted interest from researchers in a wide range of biological subdisciplines, including evolutionary genetics, behavioural ecology and, more recently, community ecology. However, the implications of frequency dependence for applied biological problems, particularly maladaptation, biological conservation and evolutionary rescue remain underexplored. The neglect of FD selection in conservation is particularly unfortunate. Classical theory, dating back to the 1940s, demonstrated that frequency dependence can either increase or decrease population fitness. These evolutionary consequences of FD selection are relevant to modern concerns about population persistence and the capacity of evolution to alleviate extinction risks. But exactly when should we expect FD selection to increase versus decrease absolute fitness and population growth? And how much of an impact is FD selection expected to have on population persistence versus extinction in changing environments? The answers to these questions have implications for evolutionary rescue under climate change and may inform strategies for managing threatened populations. Here, we revisit the core theory of FD selection, reviewing classical single-locus models of population genetic change and outlining short- and long-run consequences of FD selection for the evolution of population fitness. We then develop a quantitative genetic model of evolutionary rescue in a deteriorating environment, with population persistence hinging upon the evolution of a quantitative trait subject to both frequency-dependent and frequency-independent natural selection. We discuss the empirical literature pertinent to this theory, which supports key assumptions of our model. We show that FD selection can promote population persistence when it aligns with the direction of frequency-independent selection imposed by abiotic environmental conditions. However, under most scenarios of environmental change, FD selection limits a population's evolutionary responsiveness to changing conditions and narrows the rate of environmental change that is evolutionarily tolerable.
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Affiliation(s)
- Erik I. Svensson
- Evolutionary Ecology UnitDepartment of BiologyLund UniversityLundSweden
| | - Tim Connallon
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
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14
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Theodosiou L, Hiltunen T, Becks L. The role of stressors in altering eco‐evolutionary dynamics. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Loukas Theodosiou
- Community Dynamics GroupMax Planck Institute for Evolutionary Biology Plön Germany
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary Biology Plön Germany
| | - Teppo Hiltunen
- Department of MicrobiologyUniversity of Helsinki Helsinki Finland
- Department of BiologyUniversity of Turku Turku Finland
| | - Lutz Becks
- Community Dynamics GroupMax Planck Institute for Evolutionary Biology Plön Germany
- Limnology ‐ Aquatic Ecology and Evolution, Limnological InstituteUniversity of Konstanz Konstanz Germany
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15
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Endriss SB, Vahsen ML, Bitume EV, Grey Monroe J, Turner KG, Norton AP, Hufbauer RA. The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours. Ecol Lett 2018; 22:45-55. [PMID: 30450720 DOI: 10.1111/ele.13166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/03/2018] [Accepted: 08/30/2018] [Indexed: 12/31/2022]
Abstract
Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found that individuals dispersed especially far when exposed to a poor environment as adults if their phenotype, or even one-third of their neighbours' phenotypes, were shaped by a poor environment as juveniles. Juvenile environment therefore shapes dispersal both directly, by influencing phenotype, as well as indirectly, by influencing the external social environment. Thus, the juvenile environment of even a minority of individuals in a group can influence the dispersal of the entire group.
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Affiliation(s)
- Stacy B Endriss
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Megan L Vahsen
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Ellyn V Bitume
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Exotic and Invasive Weeds Research Unit, U.S. Department of Agriculture - Agricultural Research Service, Albany, CA, USA
| | - J Grey Monroe
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Kathryn G Turner
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.,Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Andrew P Norton
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Ruth A Hufbauer
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
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16
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Caution, Overload: The Troubled Past of Genetic Load. Genetics 2018; 210:747-755. [PMID: 30401761 DOI: 10.1534/genetics.118.301093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/22/2018] [Indexed: 11/18/2022] Open
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17
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Christie MR, Searle CL. Evolutionary rescue in a host-pathogen system results in coexistence not clearance. Evol Appl 2018; 11:681-693. [PMID: 29875810 PMCID: PMC5979755 DOI: 10.1111/eva.12568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/17/2017] [Indexed: 01/14/2023] Open
Abstract
The evolutionary rescue of host populations may prevent extinction from novel pathogens. However, the conditions that facilitate rapid evolution of hosts, in particular the population variation in host susceptibility, and the effects of host evolution in response to pathogens on population outcomes remain largely unknown. We constructed an individual-based model to determine the relationships between genetic variation in host susceptibility and population persistence in an amphibian-fungal pathogen (Batrachochytrium dendrobatidis) system. We found that host populations can rapidly evolve reduced susceptibility to a novel pathogen and that this rapid evolution led to a 71-fold increase in the likelihood of host-pathogen coexistence. However, the increased rates of coexistence came at a cost to host populations; fewer populations cleared infection, population sizes were depressed, and neutral genetic diversity was lost. Larger adult host population sizes and greater adaptive genetic variation prior to the onset of pathogen introduction led to substantially reduced rates of extinction, suggesting that populations with these characteristics should be prioritized for conservation when species are threatened by novel infectious diseases.
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Affiliation(s)
- Mark Redpath Christie
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
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18
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Stewart GS, Morris MR, Genis AB, Szűcs M, Melbourne BA, Tavener SJ, Hufbauer RA. The power of evolutionary rescue is constrained by genetic load. Evol Appl 2017; 10:731-741. [PMID: 28717392 PMCID: PMC5511356 DOI: 10.1111/eva.12489] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/11/2017] [Indexed: 12/31/2022] Open
Abstract
The risk of extinction faced by small isolated populations in changing environments can be reduced by rapid adaptation and subsequent growth to larger, less vulnerable sizes. Whether this process, called evolutionary rescue, is able to reduce extinction risk and sustain population growth over multiple generations is largely unknown. To understand the consequences of adaptive evolution as well as maladaptive processes in small isolated populations, we subjected experimental Tribolium castaneum populations founded with 10 or 40 individuals to novel environments, one more favorable, and one resource poor, and either allowed evolution, or constrained it by replacing individuals one-for-one each generation with those from a large population maintained in the natal environment. Replacement individuals spent one generation in the target novel environment before use to standardize effects due to the parental environment. After eight generations we mixed a subset of surviving populations to facilitate admixture, allowing us to estimate drift load by comparing performance of mixed to unmixed groups. Evolving populations had reduced extinction rates, and increased population sizes in the first four to five generations compared to populations where evolution was constrained. Performance of evolving populations subsequently declined. Admixture restored their performance, indicating high drift load that may have overwhelmed the beneficial effects of adaptation in evolving populations. Our results indicate that evolution may quickly reduce extinction risk and increase population sizes, but suggest that relying solely on adaptation from standing genetic variation may not provide long-term benefits to small isolated populations of diploid sexual species, and that active management facilitating gene flow may be necessary for longer term persistence.
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Affiliation(s)
- Gavin S. Stewart
- Department of MathematicsColorado State UniversityFort CollinsCOUSA
- Department of MathematicsCourant Institute of Mathematical SciencesNew YorkNYUSA
| | - Madeline R. Morris
- Department of Biomedical SciencesColorado State UniversityFort CollinsCOUSA
| | | | - Marianna Szűcs
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
| | - Brett A. Melbourne
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
| | - Simon J. Tavener
- Department of MathematicsColorado State UniversityFort CollinsCOUSA
| | - Ruth A. Hufbauer
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsCOUSA
- Centre de Biologie pour la Gestion des Populations (INRA, Montpellier SupAgro)Montferrier‐sur‐Lez CedexFrance
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