1
|
Conner LM, Goedert D, Fitzpatrick SW, Fearnley A, Gallagher EL, Peterman JD, Forgione ME, Kokosinska S, Hamilton M, Masala LA, Merola N, Rico H, Samma E, Brady SP. Population origin and heritable effects mediate road salt toxicity and thermal stress in an amphibian. CHEMOSPHERE 2024; 357:141978. [PMID: 38608774 DOI: 10.1016/j.chemosphere.2024.141978] [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: 10/07/2023] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Human impacts on wild populations are numerous and extensive, degrading habitats and causing population declines across taxa. Though these impacts are often studied individually, wild populations typically face suites of stressors acting concomitantly, compromising the fitness of individuals and populations in ways poorly understood and not easily predicted by the effects of any single stressor. Developing understanding of the effects of multiple stressors and their potential interactions remains a critical challenge in environmental biology. Here, we focus on assessing the impacts of two prominent stressors associated with anthropogenic activities that affect many organisms across the planet - elevated salinity (e.g., from road de-icing salt) and temperature (e.g. from climate change). We examined a suite of physiological traits and components of fitness across populations of wood frogs originating from ponds that differ in their proximity to roads and thus their legacy of exposure to pollution from road salt. When experimentally exposed to road salt, wood frogs showed reduced survival (especially those from ponds adjacent to roads), divergent developmental rates, and reduced longevity. Family-level effects mediated these outcomes, but high salinity generally eroded family-level variance. When combined, exposure to both temperature and salt resulted in very low survival, and this effect was strongest in roadside populations. Taken together, these results suggest that temperature is an important stressor capable of exacerbating impacts from a prominent contaminant confronting many freshwater organisms in salinized habitats. More broadly, it appears likely that toxicity might often be underestimated in the absence of multi-stressor approaches.
Collapse
Affiliation(s)
- Lauren M Conner
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Debora Goedert
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA; Department of Integrative Biology, Michigan State University, East Lansing, MI, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Amber Fearnley
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Emma L Gallagher
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Jessica D Peterman
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Mia E Forgione
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Sophia Kokosinska
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Malik Hamilton
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Lydia A Masala
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Neil Merola
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Hennesy Rico
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Eman Samma
- Southern Connecticut State University, Biology Department, New Haven, CT, USA
| | - Steven P Brady
- Southern Connecticut State University, Biology Department, New Haven, CT, USA.
| |
Collapse
|
2
|
Yoshiyama Y, Wakabayashi Y, Mercer KL, Kawabata S, Kobayashi T, Tabuchi T, Yamori W. Natural genetic variation in dynamic photosynthesis is correlated with stomatal anatomical traits in diverse tomato species across geographical habitats. JOURNAL OF EXPERIMENTAL BOTANY 2024:erae082. [PMID: 38606772 DOI: 10.1093/jxb/erae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/23/2024] [Indexed: 04/13/2024]
Abstract
Plants grown under field conditions experience fluctuating light. Understanding the natural genetic variations for a similarly dynamic photosynthetic response among untapped germplasm resources, as well as the underlying mechanisms, may offer breeding strategies to improve production using molecular approaches. Here, we measured gas exchange under fluctuating light, along with stomatal density and size, in eight wild tomato species and two tomato cultivars. The photosynthetic induction response showed significant diversity, with some wild species having faster induction rates than the two cultivars. Species with faster photosynthetic induction rates had higher daily integrated photosynthesis, but lower average water use efficiency because of high stomatal conductance under natural fluctuating light. The variation in photosynthetic induction was closely associated with the speed of stomatal responses, highlighting its critical role in maximizing photosynthesis under fluctuating light conditions. Moreover, stomatal size was negatively correlated with stomatal density within a species, and plants with smaller stomata at a higher density had a quicker photosynthetic response than those with larger stomata at lower density. Our findings show that the response of stomatal conductance plays a pivotal role in photosynthetic induction, with smaller stomata at higher density proving advantageous for photosynthesis under fluctuating light in tomato species. The interspecific variation in the rate of stomatal responses could offer an untapped resource for optimizing dynamic photosynthetic responses under field conditions.
Collapse
Affiliation(s)
- Yugo Yoshiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| | - Yu Wakabayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| | - Kristin L Mercer
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
- Ohio State University, Department of Horticulture and Crop Science, Columbus, OH, USA
| | - Saneyuki Kawabata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| | - Takayuki Kobayashi
- Department of Advanced Food Sciences, College of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Toshihito Tabuchi
- Department of Advanced Food Sciences, College of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Wataru Yamori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| |
Collapse
|
3
|
Kehlet-Delgado H, Montoya AP, Jensen KT, Wendlandt CE, Dexheimer C, Roberts M, Torres Martínez L, Friesen ML, Griffitts JS, Porter SS. The evolutionary genomics of adaptation to stress in wild rhizobium bacteria. Proc Natl Acad Sci U S A 2024; 121:e2311127121. [PMID: 38507447 PMCID: PMC10990125 DOI: 10.1073/pnas.2311127121] [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: 07/05/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024] Open
Abstract
Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.
Collapse
Affiliation(s)
| | | | - Kyson T. Jensen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT84602
| | | | | | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, WA98686
| | | | - Maren L. Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA99164
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA99164
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT84602
| | - Stephanie S. Porter
- School of Biological Sciences, Washington State University, Vancouver, WA98686
| |
Collapse
|
4
|
Yoccoz NG. Genetic basis and trade-offs of cold acclimation. Proc Natl Acad Sci U S A 2024; 121:e2400501121. [PMID: 38381781 DOI: 10.1073/pnas.2400501121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Affiliation(s)
- Nigel G Yoccoz
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, University of Tromsø The Arctic University of Norway, Tromsø N-9037, Norway
| |
Collapse
|
5
|
Candido-Ribeiro R, Aitken SN. Weak local adaptation to drought in seedlings of a widespread conifer. THE NEW PHYTOLOGIST 2024; 241:2395-2409. [PMID: 38247230 DOI: 10.1111/nph.19543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well-characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests. We used a large-scale common garden drought-to-death experiment to assess range-wide variation in drought tolerance, measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (Pseudotsuga menziesii var. menziesii and var. glauca). Local adaptation to drought was weak in var. glauca and nearly absent in menziesii. Var. glauca showed higher tolerance to drought but slower growth than var. menziesii. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. menziesii in response to extreme drought. Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.
Collapse
Affiliation(s)
- Rafael Candido-Ribeiro
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
6
|
Lee G, Sanderson BJ, Ellis TJ, Dilkes BP, McKay JK, Ågren J, Oakley CG. A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation. Proc Natl Acad Sci U S A 2024; 121:e2317461121. [PMID: 38289961 PMCID: PMC10861903 DOI: 10.1073/pnas.2317461121] [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: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-y mean fitness and fitness components at the native field sites by comparing near-isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene-edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene-edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.
Collapse
Affiliation(s)
- Gwonjin Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Brian J. Sanderson
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Thomas J. Ellis
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, UppsalaSE-752 36, Sweden
| | - Brian P. Dilkes
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
- Department of Biochemistry, Purdue University, West Lafayette, IN47907
| | - John K. McKay
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO80523
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, UppsalaSE-752 36, Sweden
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| |
Collapse
|
7
|
James ME, Ortiz-Barrientos D. The genomic consequences of selection across development. Mol Ecol 2024; 33:e17280. [PMID: 38247305 DOI: 10.1111/mec.17280] [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: 09/25/2023] [Revised: 01/01/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Understanding how natural selection drives diversification in nature has been at the forefront of biological research for over a century. The main idea is simple: natural selection favours individuals best suited to pass on their genes. However, the journey from birth to reproduction is complex as organisms experience multiple developmental stages, each influenced by genetic and environmental factors (Orr, 2009). These complexities compound even further as each stage of development might be governed by a unique underlying set of alleles and genes. In this issue of Molecular Ecology, Goebl et al. (2022) examine the role of natural selection in driving ecotypic divergence across different life history stages of the prairie sunflower Helianthus petiolaris. The authors used reciprocal transplant experiments, demographic models, and genomic sequencing to explore fitness variation across developmental stages. They show how natural selection impacts population divergence across multiple life history stages and evaluate the resulting allele frequency changes. Goebl et al. link these results to the role of chromosomal inversions, thus furthering our understanding of how ecological divergence proceeds in the face of gene flow. Below, we explore these results in detail and complement their interpretation by considering the evolution of genetic correlations amongst traits governing fitness.
Collapse
Affiliation(s)
- Maddie E James
- School of the Environment, The University of Queensland, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, The University of Queensland, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD, Australia
| |
Collapse
|
8
|
Smith DD, Adams MA, Salvi AM, Krieg CP, Ané C, McCulloh KA, Givnish TJ. Ecophysiological adaptations shape distributions of closely related trees along a climatic moisture gradient. Nat Commun 2023; 14:7173. [PMID: 37935674 PMCID: PMC10630429 DOI: 10.1038/s41467-023-42352-w] [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: 03/14/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
Tradeoffs between the energetic benefits and costs of traits can shape species and trait distributions along environmental gradients. Here we test predictions based on such tradeoffs using survival, growth, and 50 photosynthetic, hydraulic, and allocational traits of ten Eucalyptus species grown in four common gardens along an 8-fold gradient in precipitation/pan evaporation (P/Ep) in Victoria, Australia. Phylogenetically structured tests show that most trait-environment relationships accord qualitatively with theory. Most traits appear adaptive across species within gardens (indicating fixed genetic differences) and within species across gardens (indicating plasticity). However, species from moister climates have lower stomatal conductance than others grown under the same conditions. Responses in stomatal conductance and five related traits appear to reflect greater mesophyll photosynthetic sensitivity of mesic species to lower leaf water potential. Our data support adaptive cross-over, with realized height growth of most species exceeding that of others in climates they dominate. Our findings show that pervasive physiological, hydraulic, and allocational adaptations shape the distributions of dominant Eucalyptus species along a subcontinental climatic moisture gradient, driven by rapid divergence in species P/Ep and associated adaptations.
Collapse
Affiliation(s)
- Duncan D Smith
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Faculty of Science, Engineering, & Technology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia.
- School of Ecosystem and Forest Sciences, University of Melbourne, Creswick, VIC, 3363, Australia.
| | - Mark A Adams
- Faculty of Science, Engineering, & Technology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Amanda M Salvi
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christopher P Krieg
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
9
|
Wessinger CA, Katzer AM, Hime PM, Rausher MD, Kelly JK, Hileman LC. A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds. PLoS Biol 2023; 21:e3002294. [PMID: 37769035 PMCID: PMC10538765 DOI: 10.1371/journal.pbio.3002294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
In the formation of species, adaptation by natural selection generates distinct combinations of traits that function well together. The maintenance of adaptive trait combinations in the face of gene flow depends on the strength and nature of selection acting on the underlying genetic loci. Floral pollination syndromes exemplify the evolution of trait combinations adaptive for particular pollinators. The North American wildflower genus Penstemon displays remarkable floral syndrome convergence, with at least 20 separate lineages that have evolved from ancestral bee pollination syndrome (wide blue-purple flowers that present a landing platform for bees and small amounts of nectar) to hummingbird pollination syndrome (bright red narrowly tubular flowers offering copious nectar). Related taxa that differ in floral syndrome offer an attractive opportunity to examine the genomic basis of complex trait divergence. In this study, we characterized genomic divergence among 229 individuals from a Penstemon species complex that includes both bee and hummingbird floral syndromes. Field plants are easily classified into species based on phenotypic differences and hybrids displaying intermediate floral syndromes are rare. Despite unambiguous phenotypic differences, genome-wide differentiation between species is minimal. Hummingbird-adapted populations are more genetically similar to nearby bee-adapted populations than to geographically distant hummingbird-adapted populations, in terms of genome-wide dXY. However, a small number of genetic loci are strongly differentiated between species. These approximately 20 "species-diagnostic loci," which appear to have nearly fixed differences between pollination syndromes, are sprinkled throughout the genome in high recombination regions. Several map closely to previously established floral trait quantitative trait loci (QTLs). The striking difference between the diagnostic loci and the genome as whole suggests strong selection to maintain distinct combinations of traits, but with sufficient gene flow to homogenize the genomic background. A surprisingly small number of alleles confer phenotypic differences that form the basis of species identity in this species complex.
Collapse
Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Amanda M. Katzer
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Mark D. Rausher
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| |
Collapse
|
10
|
Oakley CG, Schemske DW, McKay JK, Ågren J. Ecological genetics of local adaptation in Arabidopsis: An 8-year field experiment. Mol Ecol 2023; 32:4570-4583. [PMID: 37317048 DOI: 10.1111/mec.17045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3-year study, identifying one new genetic trade-off and resolving one genetic trade-off into two conditionally adaptive QTL.
Collapse
Affiliation(s)
- Christopher G Oakley
- Department of Botany and Plant Pathology, and the Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan, USA
| | - John K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| |
Collapse
|
11
|
Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proc Natl Acad Sci U S A 2023; 120:e2219835120. [PMID: 36881629 PMCID: PMC10089221 DOI: 10.1073/pnas.2219835120] [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: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.
Collapse
Affiliation(s)
- Scott T. Small
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
| | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Scott J. Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Andrew D. Kern
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Michael C. Fontaine
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
| | - Nora J. Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
| |
Collapse
|
12
|
Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
Collapse
|
13
|
Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
Collapse
Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
| |
Collapse
|