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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [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: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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Robert E, Lenz P, Bergeron Y, de Lafontaine G, Bouriaud O, Isabel N, Girardin MP. Future carbon sequestration potential in a widespread transcontinental boreal tree species: Standing genetic variation matters! GLOBAL CHANGE BIOLOGY 2024; 30:e17347. [PMID: 38822663 DOI: 10.1111/gcb.17347] [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: 09/01/2023] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/03/2024]
Abstract
Climate change (CC) necessitates reforestation/afforestation programs to mitigate its impacts and maximize carbon sequestration. But comprehending how tree growth, a proxy for fitness and resilience, responds to CC is critical to maximize these programs' effectiveness. Variability in tree response to CC across populations can notably be influenced by the standing genetic variation encompassing both neutral and adaptive genetic diversity. Here, a framework is proposed to assess tree growth potential at the population scale while accounting for standing genetic variation. We applied this framework to black spruce (BS, Picea mariana [Mill] B.S.P.), with the objectives to (1) determine the key climate variables having impacted BS growth response from 1974 to 2019, (2) examine the relative roles of local adaptation and the phylogeographic structure in this response, and (3) project BS growth under two Shared Socioeconomic Pathways while taking standing genetic variation into account. We modeled growth using a machine learning algorithm trained with dendroecological and genetic data obtained from over 2600 trees (62 populations divided in three genetic clusters) in four 48-year-old common gardens, and simulated growth until year 2100 at the common garden locations. Our study revealed that high summer and autumn temperatures negatively impacted BS growth. As a consequence of warming, this species is projected to experience a decline in growth by the end of the century, suggesting maladaptation to anticipated CC and a potential threat to its carbon sequestration capacity. This being said, we observed a clear difference in response to CC within and among genetic clusters, with the western cluster being more impacted than the central and eastern clusters. Our results show that intraspecific genetic variation, notably associated with the phylogeographic structure, must be considered when estimating the response of widespread species to CC.
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Affiliation(s)
- Etienne Robert
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| | - Patrick Lenz
- Natural Resources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, Quebec City, Quebec, Canada
| | - Yves Bergeron
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Quebec, Canada
- Institut de Recherche Sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, Québec, Canada
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Olivier Bouriaud
- Ștefan Cel Mare University of Suceava, Suceava, Romania
- IGN, ENSG, Laboratoire d'Inventaire Forestier - LIF, Nancy, France
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| | - Martin P Girardin
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada
- Institut de Recherche Sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, Québec, Canada
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3
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Danzey LM, Briceño VF, Cook AM, Nicotra AB, Peyre G, Rossetto M, Yap JYS, Leigh A. Environmental and Biogeographic Drivers behind Alpine Plant Thermal Tolerance and Genetic Variation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1271. [PMID: 38732486 PMCID: PMC11085172 DOI: 10.3390/plants13091271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
In alpine ecosystems, elevation broadly functions as a steep thermal gradient, with plant communities exposed to regular fluctuations in hot and cold temperatures. These conditions lead to selective filtering, potentially contributing to species-level variation in thermal tolerance and population-level genetic divergence. Few studies have explored the breadth of alpine plant thermal tolerances across a thermal gradient or the underlying genetic variation thereof. We measured photosystem heat (Tcrit-hot) and cold (Tcrit-cold) thresholds of ten Australian alpine species across elevation gradients and characterised their neutral genetic variation. To reveal the biogeographical drivers of present-day genetic signatures, we also reconstructed temporal changes in habitat suitability across potential distributional ranges. We found intraspecific variation in thermal thresholds, but this was not associated with elevation, nor underpinned by genetic differentiation on a local scale. Instead, regional population differentiation and considerable homozygosity within populations may, in part, be driven by distributional contractions, long-term persistence, and migrations following habitat suitability. Our habitat suitability models suggest that cool-climate-distributed alpine plants may be threatened by a warming climate. Yet, the observed wide thermal tolerances did not reflect this vulnerability. Conservation efforts should seek to understand variations in species-level thermal tolerance across alpine microclimates.
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Affiliation(s)
- Lisa M. Danzey
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway, NSW 2007, Australia;
| | - Verónica F. Briceño
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; (V.F.B.); (A.B.N.)
| | - Alicia M. Cook
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway, NSW 2007, Australia;
| | - Adrienne B. Nicotra
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; (V.F.B.); (A.B.N.)
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogota 111711, Colombia;
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Sydney, NSW 2000, Australia; (M.R.); (J.-Y.S.Y.)
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jia-Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Sydney, NSW 2000, Australia; (M.R.); (J.-Y.S.Y.)
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrea Leigh
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; (V.F.B.); (A.B.N.)
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Chen B, Wang M, Guo Y, Zhang Z, Zhou W, Cao L, Zhang T, Ali S, Xie L, Li Y, Zinta G, Sun S, Zhang Q. Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana. Mol Ecol 2024:e17356. [PMID: 38634782 DOI: 10.1111/mec.17356] [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: 01/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.
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Affiliation(s)
- Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou, China
| | - Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yile Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zihui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shahid Ali
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Linan Xie
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuhua Li
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shanwen Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Cheng J, Zhang Z, Li Y, Zhang L, Hui M, Sha Z. Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170244. [PMID: 38278258 DOI: 10.1016/j.scitotenv.2024.170244] [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: 09/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Investigating spatial pattern of adaptive variation and its underlying processes can inform the adaptive potential distributed within species ranges, which is increasingly important in the context of a changing climate. A correct interpretation of adaptive variation pattern requires that population history and the ensuing population genetic structure are taken into account. Here we carried out such a study by integrating population genomic analyses, demographic model testing and species distribution modeling to investigate patterns and causes of adaptive differentiation in a widespread mantis shrimp, Oratosquilla oratoria, along a replicated, broad-scale temperature gradient in the northwestern Pacific (NWP). Our results supported a strong hierarchical ecogeographic structure dominated by habitat-linked divergence among O. oratoria populations accompanied with introgressive hybridization. A combined FST outlier and environmental correlation analyses revealed remarkable temperature-associated clines in allele frequency across paired North-South populations on Chinese and Japanese coasts, and identified a suite of loci associated with temperature adaptation. Further demographic model testing revealed the observed clinal variation derived partly from Pleistocene divergence followed by recent secondary contact. More importantly, the likelihood of hybridization is predicted to increase as climate change progresses, which would break barriers to gene flow and enable the spread of adaptive genetic variation. These results support that not only is temperature-driven adaptive differentiation occurs in O. oratoria but that such pattern is likely attributed to ancient adaptive variation, sustained by contemporary ocean conditions and a semi-permeable barrier to gene flow maintained by selection. They moreover provide genomic insights into the distribution of adaptive potential across O. oratoria' s species range. This work can serve as a case study to characterize adaptive diversity of marine species in the NWP by integrating environmental and genetic data at temporal and spatial scales in a population genomic framework, which would improve management and conservation actions under climate change.
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Affiliation(s)
- Jiao Cheng
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510275, China
| | - Yulong Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liwen Zhang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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6
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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Silvestro R, Mura C, Alano Bonacini D, de Lafontaine G, Faubert P, Mencuccini M, Rossi S. Local adaptation shapes functional traits and resource allocation in black spruce. Sci Rep 2023; 13:21257. [PMID: 38040772 PMCID: PMC10692160 DOI: 10.1038/s41598-023-48530-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Climate change is rapidly altering weather patterns, resulting in shifts in climatic zones. The survival of trees in specific locations depends on their functional traits. Local populations exhibit trait adaptations that ensure their survival and accomplishment of growth and reproduction processes during the growing season. Studying these traits offers valuable insights into species responses to present and future environmental conditions, aiding the implementation of measures to ensure forest resilience and productivity. This study investigates the variability in functional traits among five black spruce (Picea mariana (Mill.) B.S.P.) provenances originating from a latitudinal gradient along the boreal forest, and planted in a common garden in Quebec, Canada. We examined differences in bud phenology, growth performance, lifetime first reproduction, and the impact of a late-frost event on tree growth and phenological adjustments. The findings revealed that trees from northern sites exhibit earlier budbreak, lower growth increments, and reach reproductive maturity earlier than those from southern sites. Late-frost damage affected growth performance, but no phenological adjustment was observed in the successive year. Local adaptation in the functional traits may lead to maladaptation of black spruce under future climate conditions or serve as a potent evolutionary force promoting rapid adaptation under changing environmental conditions.
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Affiliation(s)
- R Silvestro
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada.
| | - C Mura
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
| | - D Alano Bonacini
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
| | - G de Lafontaine
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de biologie, chimie et Géographie, Centre for Northern Studies, Centre for Forest Research, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - P Faubert
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
- Carbone boréal, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H 2B1, Canada
| | - M Mencuccini
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), 08193, Bellaterra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluis Companys 23, 08010, Barcelona, Spain
| | - S Rossi
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
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8
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Marková S, Lanier HC, Escalante MA, da Cruz MOR, Horníková M, Konczal M, Weider LJ, Searle JB, Kotlík P. Local adaptation and future climate vulnerability in a wild rodent. Nat Commun 2023; 14:7840. [PMID: 38030627 PMCID: PMC10686993 DOI: 10.1038/s41467-023-43383-z] [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: 06/02/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
As climate change continues, species pushed outside their physiological tolerance limits must adapt or face extinction. When change is rapid, adaptation will largely harness ancestral variation, making the availability and characteristics of that variation of critical importance. Here, we used whole-genome sequencing and genetic-environment association analyses to identify adaptive variation and its significance in the context of future climates in a small Palearctic mammal, the bank vole (Clethrionomys glareolus). We found that peripheral populations of bank vole in Britain are already at the extreme bounds of potential genetic adaptation and may require an influx of adaptive variation in order to respond. Analyses of adaptive loci suggest regional differences in climate variables select for variants that influence patterns of population adaptive resilience, including genes associated with antioxidant defense, and support a pattern of thermal/hypoxic cross-adaptation. Our findings indicate that understanding potential shifts in genomic composition in response to climate change may be key to predicting species' fate under future climates.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Hayley C Lanier
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Marcos O R da Cruz
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Mateusz Konczal
- Faculty of Biology, Evolutionary Biology Group, Adam Mickiewicz University, Poznań, Poland
| | - Lawrence J Weider
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic.
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9
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Hankin LE, Leger EA, Bisbing SM. Reforestation of high elevation pines: Direct seeding success depends on seed source and sowing environment. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2897. [PMID: 37305925 DOI: 10.1002/eap.2897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/10/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Forest persistence in regions impacted by increasing water and temperature stress will depend upon species' ability to either rapidly adjust to novel conditions or migrate to track ecological niches. Predicted, rapid climate change is likely to outpace the adaptive and migratory capacity of long-lived isolated tree species, and reforestation may be critical to species' persistence. Facilitating persistence both within and beyond a species' range requires identification of seed lots best adapted to the current and future conditions predicted with rapid climate change. We evaluate variation in emergent seedling performance that leads to differential survival among species and populations for three high elevation five-needle pines. We paired a fully reciprocal field common garden experiment with a greenhouse common garden study to (1) quantify variation in seedling emergence and functional traits, (2) ask how functional traits affect performance under different establishment conditions, and (3) evaluate whether trait and performance variation demonstrates local adaptation and plasticity. Among study species-limber, Great Basin bristlecone, and whitebark pines-we found divergence in emergence and functional traits, though soil moisture was the strongest driver of seedling emergence and abundance across all species. Generalist limber pine had a clear emergence advantage as well as traits associated with drought adaptation, while edaphic specialist bristlecone pine was characterized by low emergence yet high early survival once established. Despite evidence for edaphic specialization, soil characteristics alone did not explain bristlecone success. Across species, trait-environment relationships provided some evidence for local adaptation in drought-adapted traits, but we found no evidence of local adaptation in emergence or survival at this early life stage. For managers looking to promote persistence, sourcing seed from drier environments is likely to impart greater drought resistance into reforestation efforts through strategies such as greater root investment, increasing the probability of early seedling survival. This research demonstrates, through a rigorous reciprocal transplant experimental design, that it may be possible to select climate- and soil-appropriate seed sources for reforestation. However, planting success will ultimately rely on a suitable establishment environment, requiring careful consideration of interannual climate variability for management interventions in these climate and disturbance-impacted tree species.
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Affiliation(s)
- Lacey E Hankin
- Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno, Nevada, USA
- Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Elizabeth A Leger
- Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
- Department of Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Sarah M Bisbing
- Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno, Nevada, USA
- Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
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10
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S Raposo D, A Zufall R, Caruso A, Titelboim D, Abramovich S, Hassenrück C, Kucera M, Morard R. Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction. Sci Rep 2023; 13:12578. [PMID: 37537233 PMCID: PMC10400638 DOI: 10.1038/s41598-023-39652-y] [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: 10/04/2022] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Among the most successful Lessepsian invaders is the symbiont-bearing benthic foraminifera Amphistegina lobifera. In its newly conquered habitat, this prolific calcifier and ecosystem engineer is exposed to environmental conditions that exceed the range of its native habitat. To disentangle which processes facilitated the invasion success of A. lobifera into the Mediterranean Sea we analyzed a ~ 1400 bp sequence fragment covering the SSU and ITS gene markers to compare the populations from its native regions and along the invasion gradient. The genetic variability was studied at four levels: intra-genomic, population, regional and geographical. We observed that the invasion is not associated with genetic differentiation, but the invasive populations show a distinct suppression of intra-genomic variability among the multiple copies of the rRNA gene. A reduced genetic diversity compared to the Indopacific is observed already in the Red Sea populations and their high dispersal potential into the Mediterranean appears consistent with a bridgehead effect resulting from the postglacial expansion from the Indian Ocean into the Red Sea. We conclude that the genetic structure of the invasive populations reflects two processes: high dispersal ability of the Red Sea source population pre-adapted to Mediterranean conditions and a likely suppression of sexual reproduction in the invader. This discovery provides a new perspective on the cost of invasion in marine protists: The success of the invasive A. lobifera in the Mediterranean Sea comes at the cost of abandonment of sexual reproduction.
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Affiliation(s)
- Débora S Raposo
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany.
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, USA
| | - Antonio Caruso
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - Danna Titelboim
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Sigal Abramovich
- Department of Earth and Environmental Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Christiane Hassenrück
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Warnemünde, Germany
| | - Michal Kucera
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany
| | - Raphaël Morard
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany
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11
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Evans A, de Kort H, Brys R, Duffy KJ, Jersáková J, Kull T, Selosse MA, Tsiftsis S, Minasiewicz J, Jacquemyn H. Historical biogeography and local adaptation explain population genetic structure in a widespread terrestrial orchid. ANNALS OF BOTANY 2023; 131:623-634. [PMID: 36680796 PMCID: PMC10147325 DOI: 10.1093/aob/mcad010] [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: 12/02/2022] [Accepted: 01/11/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Historical changes in environmental conditions and colonization-extinction dynamics have a direct impact on the genetic structure of plant populations. However, understanding how past environmental conditions influenced the evolution of species with high gene flow is challenging when signals for genetic isolation and adaptation are swamped by gene flow. We investigated the spatial distribution and genetic structure of the widespread terrestrial orchid Epipactis helleborine to identify glacial refugia, characterize postglacial population dynamics and assess its adaptive potential. METHODS Ecological niche modelling was used to locate possible glacial refugia and postglacial recolonization opportunities of E. helleborine. A large single-nucleotide polymorphism (SNP) dataset obtained through genotyping by sequencing was used to define population genetic diversity and structure and to identify sources of postglacial gene flow. Outlier analyses were used to elucidate how adaptation to the local environment contributed to population divergence. KEY RESULTS The distribution of climatically suitable areas was restricted during the Last Glacial Maximum to the Mediterranean, south-western Europe and small areas in the Alps and Carpathians. Within-population genetic diversity was high in E. helleborine (mean expected heterozygosity, 0.373 ± 0.006; observed heterozygosity, 0.571 ± 0.012; allelic richness, 1.387 ± 0.007). Italy and central Europe are likely to have acted as important genetic sources during postglacial recolonization. Adaptive SNPs were associated with temperature, elevation and precipitation. CONCLUSIONS Forests in the Mediterranean and Carpathians are likely to have acted as glacial refugia for Epipactis helleborine. Postglacial migration northwards and to higher elevations resulted in the dispersal and diversification of E. helleborine in central Europe and Italy, and to geographical isolation and divergent adaptation in Greek and Italian populations. Distinguishing adaptive from neutral genetic diversity allowed us to conclude that E. helleborine has a high adaptive potential to climate change and demonstrates that signals of adaptation and historical isolation can be identified even in species with high gene flow.
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Affiliation(s)
- Alexandra Evans
- Department of Biology, Plant Conservation and Population Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Hanne de Kort
- Department of Biology, Plant Conservation and Population Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rein Brys
- Research Institute for Forest and Nature, Geraardsbergen, Belgium
| | - Karl J Duffy
- Department of Biology, University of Naples Federico II, Complesso Monte Sant’Angelo, Naples 80126, Italy
| | - Jana Jersáková
- Department of Biology of Ecosystems, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tiiu Kull
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi, 51014 Tartu, Estonia
| | - Marc-André Selosse
- Institut Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Spyros Tsiftsis
- Department of Forest and Natural Environment Sciences, International Hellenic University, GR-66132, Drama, Greece
| | - Julita Minasiewicz
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, Katholieke Universiteit Leuven, Leuven, Belgium
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12
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Luqman H, Wegmann D, Fior S, Widmer A. Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles. Nat Commun 2023; 14:1080. [PMID: 36841810 PMCID: PMC9968346 DOI: 10.1038/s41467-023-36631-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Quaternary climate fluctuations drove many species to shift their geographic ranges, in turn shaping their genetic structures. Recently, it has been argued that adaptation may have accompanied species range shifts via the "sieving" of genotypes during colonisation and establishment. However, this has not been directly demonstrated, and knowledge remains limited on how different evolutionary forces, which are typically investigated separately, interacted to jointly mediate species responses to past climatic change. Here, through whole-genome re-sequencing of over 1200 individuals of the carnation Dianthus sylvestris coupled with integrated population genomic and gene-environment models, we reconstruct the past neutral and adaptive landscape of this species as it was shaped by the Quaternary glacial cycles. We show that adaptive responses emerged concomitantly with the post-glacial range shifts and expansions of this species in the last 20 thousand years. This was due to the heterogenous sieving of adaptive alleles across space and time, as populations expanded out of restrictive glacial refugia into the broader and more heterogeneous range of habitats available in the present-day inter-glacial. Our findings reveal a tightly-linked interplay of migration and adaptation under past climate-induced range shifts, which we show is key to understanding the spatial patterns of adaptive variation we see in species today.
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Affiliation(s)
- Hirzi Luqman
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland. .,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Simone Fior
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
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13
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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14
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Pelletier E, de Lafontaine G. Jack pine of all trades: Deciphering intraspecific variability of a key adaptive trait at the rear edge of a widespread fire-embracing North American conifer. AMERICAN JOURNAL OF BOTANY 2023; 110:e16111. [PMID: 36462149 DOI: 10.1002/ajb2.16111] [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: 06/25/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Understanding mechanisms fostering long-term persistence of marginal populations should provide key insights about species resilience facing climate change. Cone serotiny is a key adaptive trait in Pinus banksiana (jack pine), which shows phenotypic variation according to the fire regime. Compared to range-core populations within the fire-prone boreal forest, low and variable serotiny in rear-edge populations suggest local adaptation to uncommon and unpredictable wildfire regime. We assessed environmental/physiological factors that might modulate intraspecific variation in cone serotiny. METHODS We experimentally subjected closed cones to incrementing temperatures, then tested seed germination to determine whether and how various ecological factors (cone age, branch height, tree size, tree age) are related to cone dehiscence and seed viability in jack pines from rear-edge and range-core populations in eastern Canada. RESULTS Cones from rear-edge populations dehisce at a lower opening temperature, which increases with cone age. Cones from range-core stands open at a more constant, yet higher temperature. Cones from rear-edge stands take between 13 and 27 years to reach the level of serotiny achieved at the range core. At the rear edge, seed viability is steady (51%), whereas it decreases from 70% to 30% in 20 years at the range core. CONCLUSIONS We inferred the mechanisms of a bet-hedging strategy in rear-edge populations, which ensures steady recruitment during fire-free intervals and successful postfire regeneration. This capacity to cope with infrequent and unpredictable fire regime should increase the resilience of jack pine populations as global changes alter fire dynamics of the boreal forest.
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Affiliation(s)
- Emmanuelle Pelletier
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de biologie, chimie et géographie, Centre for Northern Studies, Centre for Forest Research, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de biologie, chimie et géographie, Centre for Northern Studies, Centre for Forest Research, Université du Québec à Rimouski, Rimouski, Québec, Canada
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15
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Gerschwitz‐Eidt MA, Dillenberger MS, Kadereit JW. Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade-dwelling species. Ecol Evol 2023; 13:e9728. [PMID: 36636428 PMCID: PMC9829489 DOI: 10.1002/ece3.9728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA-sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well-known refugia. We hypothesize that low light requirements evolved when species persisting in cold-stage refugia were forced into marginal habitats by more competitive warm-stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.
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Affiliation(s)
- Michael A. Gerschwitz‐Eidt
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐UniversitätMainzGermany
| | - Markus S. Dillenberger
- Institut für Biologie, AG Systematische Botanik und Pflanzengeographie, Freie Universität BerlinBerlinGermany
| | - Joachim W. Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐UniversitätMainzGermany,Present address:
Systematik, Biodiversität und Evolution der PflanzenLudwig‐Maximilians‐Universität MünchenMunichGermany
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16
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Napier JD, Heckman RW, Juenger TE. Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity. THE PLANT CELL 2023; 35:109-124. [PMID: 36342220 PMCID: PMC9806611 DOI: 10.1093/plcell/koac322] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 05/13/2023]
Abstract
Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.
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Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
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17
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Worth JRP, Shitara T, Kitamura K, Kikuchi S, Kanetani S, Matsui T, Uchiyama K, Tomaru N. Low‐elevation warm‐edge
Fagus crenata
populations in the core of the species range are glacial relicts with high conservation value. Ecol Res 2022. [DOI: 10.1111/1440-1703.12378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- James R. P. Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
| | - Takuto Shitara
- Institute of Agriculture Tokyo University of Agriculture and Technology Fuchu‐shi, Tokyo Japan
| | - Keiko Kitamura
- Hokkaido Research Centre, Forestry and Forest Products Research Institute Forest Research and Management Organization Sapporo, Hokkaido Japan
| | - Satoshi Kikuchi
- Hokkaido Research Centre, Forestry and Forest Products Research Institute Forest Research and Management Organization Sapporo, Hokkaido Japan
| | - Seiichi Kanetani
- Kyushu Research Center Forestry and Forest Products Research Institute Chuo‐ku, Kumamoto Japan
| | - Tetsuya Matsui
- Center for Biodiversity and Climate Change, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba, Ibaraki Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences Nagoya University Chikusa‐ku, Nagoya Japan
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18
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Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat Commun 2022; 13:6541. [PMID: 36319648 PMCID: PMC9626627 DOI: 10.1038/s41467-022-34206-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.
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19
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Roesti M, Gilbert KJ, Samuk K. Chromosomal inversions can limit adaptation to new environments. Mol Ecol 2022; 31:4435-4439. [PMID: 35810344 DOI: 10.1111/mec.16609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason and use simulations to illustrate that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may contribute to the maintenance of polymorphism within species.
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Affiliation(s)
- Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Kieran Samuk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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20
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Yap JYS, Rossetto M, Das S, Wilson PD, Beaumont LJ, Henry RJ. Tracking habitat or testing its suitability? Similar distributional patterns can hide very different histories of persistence versus nonequilibrium dynamics. Evolution 2022; 76:1209-1228. [PMID: 35304742 DOI: 10.1111/evo.14460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023]
Abstract
The expansions and contractions of a species' range in response to temporal changes in selective filters leave genetic signatures that can inform a more accurate reconstruction of their evolutionary history across the landscape. After a long period of continental decline, Australian rainforests settled into localized patterns of contraction or expansion during the climatic fluctuations of the Quaternary. The environmental impacts of recurring glacial and interglacial periods also intensified the arrival of new lineages from the Sunda shelf, and it can be expected that immigrant versus locally persistent taxa responded to environmental challenges in quantifiably different manner. To investigate how such differences impact on species' distribution, we contrast landscape genomic patterns and changes in habitat availability between a species with a long continental history on Doryphora sassafras and a Sunda-derived species (Toona ciliata), across a distributional overlap. Extensive landscape-level homogeneity across chloroplast and nuclear genomes for the Sunda-derived T. ciliata, characterize the genetic signature of a very recent invasion and a rapid southern "exploratory" expansion that had not been previously recorded in the Australian flora (i.e., of Gondwanan origin or Sahul-derived). In contrast, D. sassafras is consistent with other Sahul-derived species characterized by strong geographical divergence and regional differentiation. Interestingly, our findings suggest that admixture between genetically divergent populations during expansion events might be a contributing factor to the successful colonization of novel habitats. Overall, this study identifies some of the mechanisms regulating the rearrangements in species distributions and assemblage composition that follow major environmental shifts, and reminds us how a species' current range might not necessarily define species' habitat preference, with the consequence that estimates of past or future range might not always be reliable.
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Affiliation(s)
- Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Sourav Das
- Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia.,Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia
| | - Linda J Beaumont
- Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia
| | - Robert J Henry
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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21
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Kotlík P, Marková S, Horníková M, Escalante MA, Searle JB. The Bank Vole (Clethrionomys glareolus) as a Model System for Adaptive Phylogeography in the European Theater. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The legacy of climatic changes during the Pleistocene glaciations allows inferences to be made about the patterns and processes associated with range expansion/colonization, including evolutionary adaptation. With the increasing availability of population genomic data, we have the opportunity to examine these questions in detail and in a variety of non-traditional model species. As an exemplar, here we review more than two decades of work by our group and others that illustrate the potential of a single “non-model model” mammal species - the bank vole (Clethrionomys glareolus), which is particularly well suited to illustrate the complexities that may be associated with range expansion and the power of genomics (and other datasets) to uncover them. We first summarize early phylogeographic work using mitochondrial DNA and then describe new phylogeographic insights gained from population genomic analysis of genome-wide SNP data to highlight the bank vole as one of the most compelling examples of a forest mammal, that survived in cryptic extra-Mediterranean (“northern”) glacial refugia in Europe, and as one of the species in which substantial replacement and mixing of lineages originating from different refugia occurred during end-glacial colonization. Our studies of bank vole hemoglobin structure and function, as well as our recent ecological niche modeling study examining differences among bank vole lineages, led us to develop the idea of “adaptive phylogeography.” This is what we call the study of the role of adaptive differences among populations in shaping phylogeographic patterns. Adaptive phylogeography provides a link between past population history and adaptation that can ultimately help predict the potential of future species responses to climate change. Because the bank vole is part of a community of organisms whose range has repeatedly contracted and then expanded in the past, what we learn from the bank vole will be useful for our understanding of a broad range of species.
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22
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Feng L, Du FK. Landscape Genomics in Tree Conservation Under a Changing Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:822217. [PMID: 35283901 PMCID: PMC8908315 DOI: 10.3389/fpls.2022.822217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/10/2022] [Indexed: 05/11/2023]
Abstract
Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fang K. Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Fang K. Du,
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23
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Shay JE, Pennington LK, Mandussi Montiel-Molina JA, Toews DJ, Hendrickson BT, Sexton JP. Rules of Plant Species Ranges: Applications for Conservation Strategies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.700962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Earth is changing rapidly and so are many plant species’ ranges. Here, we synthesize eco-evolutionary patterns found in plant range studies and how knowledge of species ranges can inform our understanding of species conservation in the face of global change. We discuss whether general biogeographic “rules” are reliable and how they can be used to develop adaptive conservation strategies of native plant species across their ranges. Rules considered include (1) factors that set species range limits and promote range shifts; (2) the impact of biotic interactions on species range limits; (3) patterns of abundance and adaptive properties across species ranges; (4) patterns of gene flow and their implications for genetic rescue, and (5) the relationship between range size and conservation risk. We conclude by summarizing and evaluating potential species range rules to inform future conservation and management decisions. We also outline areas of research to better understand the adaptive capacity of plants under environmental change and the properties that govern species ranges. We advise conservationists to extend their work to specifically consider peripheral and novel populations, with a particular emphasis on small ranges. Finally, we call for a global effort to identify, synthesize, and analyze prevailing patterns or rules in ecology to help speed conservation efforts.
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24
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Nelson KN, O'Dean E, Knapp EE, Parker AJ, Bisbing SM. Persistent yet vulnerable: resurvey of an Abies ecotone reveals few differences but vulnerability to climate change. Ecology 2021; 102:e03525. [PMID: 34467519 DOI: 10.1002/ecy.3525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/02/2021] [Accepted: 05/20/2021] [Indexed: 11/09/2022]
Abstract
Climate change is shifting forest tree species distributions across elevational and latitudinal gradients, and these changes are often pronounced at ecotones where species meet their climatic bounds and are replaced by other species. Using an extensive ecotone composed of lower-montane white fir (Abies concolor var. lowiana) and upper-montane red fir (Abies magnifica var. magnifica) in the central Sierra Nevada range of California, USA, we (1) examined how the demographics of the ecotone have responded to recent climate using a field observational study and a historical dataset, (2) quantified climate drivers across species life stages using contemporary demographic data, and (3) tested the potential impacts of future climate on species-specific seedling survival and growth in a fully factorial growth chamber experiment that varied temperature, growing season length, and water availability. A re-examination of the ecotone midpoint after 35 yr suggested a reduction in A. concolor sapling and tree densities and a rise in A. magnifica proportional dominance between surveys. Seedling abundances across the ecotone indicated that A. magnifica tends to dominate the regeneration layer and currently forms an important component of the seedling community at elevations below those where A. magnifica saplings or trees begin to co-dominate stands. Observational and experimental assessments suggest that temperature and precipitation serve as important drivers, differentiating A. concolor vs. A. magnifica distributions, and are primary stressors at the seedling stage. Seedlings of both species were adversely affected by experimental climate treatments, although A. concolor exhibited greater survival and a more conservative growth strategy under extreme climatic stress than A. magnifica. Projections indicate that historical climate conditions will rise by an amount greater than the ecotone's current elevational extent by the end of the 21st century. Differential drivers of species abundances suggest that the projected climate will expand conditions that promote A. concolor abundance and impede A. magnifica abundance across the ecotone; however, disturbance activity and microclimatic conditions will also influence regeneration and overstory tree dynamics. Our study demonstrates the importance of quantifying species-specific responses to climate and indicates that widespread regeneration failure may be one possible consequence in which species exhibit strong sensitivity to projected climate conditions.
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Affiliation(s)
- Kellen N Nelson
- Pacific Northwest Research Station, USDA Forest Service, 11175 Auke Lake Way, Juneau, Alaska, 99801, USA.,Department of Natural Resources & Environmental Science, University of Nevada, Reno, 1664 N. Virginia Ave, Reno, Nevada, 89557, USA
| | - Emily O'Dean
- Department of Geological Sciences and Engineering, University of Nevada, Reno, 1664 N. Virginia Ave, Reno, Nevada, 89557, USA.,Department of Natural Resource Management & Environmental Science, California Polytechnic State University, 1 Grand Ave, San Luis Obispo, California, 93407, USA
| | - Eric E Knapp
- Pacific Southwest Research Station, USDA Forest Service, 3644 Avtech Parkway, Redding, California, 96002, USA
| | - Albert J Parker
- Department of Geography, University of Georgia, Athens, Georgia, 30605, USA
| | - Sarah M Bisbing
- Department of Natural Resources & Environmental Science, University of Nevada, Reno, 1664 N. Virginia Ave, Reno, Nevada, 89557, USA
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25
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Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers. FORESTS 2021. [DOI: 10.3390/f12091164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.
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Postolache D, Oddou-Muratorio S, Vajana E, Bagnoli F, Guichoux E, Hampe A, Le Provost G, Lesur I, Popescu F, Scotti I, Piotti A, Vendramin GG. Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range. Mol Ecol 2021; 30:5029-5047. [PMID: 34383353 DOI: 10.1111/mec.16115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.
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Affiliation(s)
- D Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Romania
| | - S Oddou-Muratorio
- INRAE, URFM, Avignon, France.,ECOBIOP Université de Pau et des Pays de l'Adour, INRAE, ECOBIOP, E2S UPPA, Saint-Pée-sur-Nivelle, France
| | - E Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Firenze), Italy
| | - E Guichoux
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France
| | - A Hampe
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France
| | - G Le Provost
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France
| | - I Lesur
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France.,HelixVenture, Mérignac, France
| | - F Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Romania
| | | | - A Piotti
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Firenze), Italy
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Firenze), Italy
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27
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Genetic diversity and genetic differentiation of Megalobrama populations inferred by mitochondrial markers. Genes Genomics 2021; 43:1119-1132. [PMID: 34342875 DOI: 10.1007/s13258-021-01126-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Megalobrama is economically one of the most important freshwater fish genera in China. However, phylogenetic relationships among M. amblycephala, M. skolkovii, M. hoffmanni and M. pellegrini remain unresolved. OBJECTIVE To explore the genetic diversity and phylogenetic relationship of Megalobrama populations belonging to all four species. METHODS The concatenated sequences of mitochondrial cytochrome b (Cytb) and control region (CR) were used to analyze the genetic variation, genetic differentiation and population expansion of 15 Megalobrama populations. RESULTS The study showed that haplotype diversity and nucleotide diversity of M. hoffmanni and M. skolkovii were high, and that M. hoffmanni was the most genetically divergent of the four species. Haplotype network analysis revealed that M. hoffmanni and M. amblycephala formed a monophyletic group each, while M. skolkovii and M. pellegrini clustered together. There was a high genetic differentiation among the four Megalobrama species, and genetic distance among populations was not affected by geographical distance. Additionally, the results indicated that there was gene flow between the Liangzi Lake (LZL) population and Jinsha River Reservoir (JS) population. Also, Zhaoqing (ZQ) population of M. hoffmanni might have experienced a population expansion. CONCLUSION Our study verifies genetic diversity and differentiation of Megalobrama populations, and these findings will represent a significant contribution to the conservation and utilization of germplasm resources of Megalobrama.
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28
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Pennington LK, Slatyer RA, Ruiz-Ramos DV, Veloz SD, Sexton JP. How is adaptive potential distributed within species ranges? Evolution 2021; 75:2152-2166. [PMID: 34164814 DOI: 10.1111/evo.14292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Quantitative genetic variation (QGV) represents a major component of adaptive potential and, if reduced toward range-edge populations, could prevent a species' expansion or adaptive response to rapid ecological change. It has been hypothesized that QGV will be lower at the range edge due to small populations-often the result of poor habitat quality-and potentially decreased gene flow. However, whether central populations are higher in QGV is unknown. We used a meta-analytic approach to test for a general QGV-range position relationship, including geographic and climatic distance from range centers. We identified 35 studies meeting our criteria, yielding nearly 1000 estimates of QGV (including broad-sense heritability, narrow-sense heritability, and evolvability) from 34 species. The relationship between QGV and distance from the geographic range or climatic niche center depended on the focal trait and how QGV was estimated. We found some evidence that QGV declines from geographic centers but that it increases toward niche edges; niche and geographic distances were uncorrelated. Nevertheless, few studies have compared QGV in both central and marginal regions or environments within the same species. We call for more research in this area and discuss potential research avenues related to adaptive potential in the context of global change.
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Affiliation(s)
- Lillie K Pennington
- Environmental Systems Graduate Group, University of California, Merced, California, 95343
| | - Rachel A Slatyer
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, 53703.,Current Address: Research School of Biology, Australian National University, Acton, ACT, 2600, Australia
| | - Dannise V Ruiz-Ramos
- Life and Environmental Sciences Department, University of California, Merced, California, 95343.,Current Address: U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, 65201
| | - Samuel D Veloz
- Point Blue Conservation Science, Petaluma, California, 94954
| | - Jason P Sexton
- Life and Environmental Sciences Department, University of California, Merced, California, 95343
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29
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Escalante MA, Horníková M, Marková S, Kotlík P. Niche differentiation in a postglacial colonizer, the bank vole Clethrionomys glareolus. Ecol Evol 2021; 11:8054-8070. [PMID: 34188871 PMCID: PMC8216960 DOI: 10.1002/ece3.7637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 01/25/2023] Open
Abstract
Species-level environmental niche modeling has been crucial in efforts to understand how species respond to climate variation and change. However, species often exhibit local adaptation and intraspecific niche differences that may be important to consider in predicting responses to climate. Here, we explore whether phylogeographic lineages of the bank vole originating from different glacial refugia (Carpathian, Western, Eastern, and Southern) show niche differentiation, which would suggest a role for local adaptation in biogeography of this widespread Eurasian small mammal. We first model the environmental requirements for the bank vole using species-wide occurrences (210 filtered records) and then model each lineage separately to examine niche overlap and test for niche differentiation in geographic and environmental space. We then use the models to estimate past [Last Glacial Maximum (LGM) and mid-Holocene] habitat suitability to compare with previously hypothesized glacial refugia for this species. Environmental niches are statistically significantly different from each other for all pairs of lineages in geographic and environmental space, and these differences cannot be explained by habitat availability within their respective ranges. Together with the inability of most of the lineages to correctly predict the distributions of other lineages, these results support intraspecific ecological differentiation in the bank vole. Model projections of habitat suitability during the LGM support glacial survival of the bank vole in the Mediterranean region and in central and western Europe. Niche differences between lineages and the resulting spatial segregation of habitat suitability suggest ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole. Our study illustrates that models pooling lineages within a species may obscure the potential for different responses to climate change among populations.
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Affiliation(s)
- Marco A. Escalante
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
| | - Michaela Horníková
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Silvia Marková
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
| | - Petr Kotlík
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
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30
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Draining the Swamping Hypothesis: Little Evidence that Gene Flow Reduces Fitness at Range Edges. Trends Ecol Evol 2021; 36:533-544. [DOI: 10.1016/j.tree.2021.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 11/23/2022]
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Bontrager M, Usui T, Lee-Yaw JA, Anstett DN, Branch HA, Hargreaves AL, Muir CD, Angert AL. Adaptation across geographic ranges is consistent with strong selection in marginal climates and legacies of range expansion. Evolution 2021; 75:1316-1333. [PMID: 33885152 DOI: 10.1111/evo.14231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/14/2021] [Indexed: 12/27/2022]
Abstract
Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers toward edges. We find that populations from poleward edges perform relatively poorly, both on average across all sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have strongly adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species' niche demonstrate strong local adaptation, regardless of their geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species' ranges.
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Affiliation(s)
- Megan Bontrager
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Current Address: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Takuji Usui
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Julie A Lee-Yaw
- Department of Biological Sciences, University of Lethbridge, Lethbridge, T1K 3M4, Canada
| | - Daniel N Anstett
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Haley A Branch
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Christopher D Muir
- School of Life Sciences, University of Hawaii, Honolulu, Hawaii, 96822, United States
| | - Amy L Angert
- Departments of Botany and Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
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Bisbing SM, Urza AK, Buma BJ, Cooper DJ, Matocq M, Angert AL. Can long‐lived species keep pace with climate change? Evidence of local persistence potential in a widespread conifer. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sarah M. Bisbing
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
| | - Alexandra K. Urza
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
- Rocky Mountain Research Station USDA Forest Service Reno NV USA
| | - Brian J. Buma
- Department of Integrative Biology University of Colorado Denver CO USA
| | - David J. Cooper
- Department of Forest and Rangeland Stewardship & Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - Marjorie Matocq
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
| | - Amy L. Angert
- Departments of Botany and Zoology University of British Columbia Vancouver BC Canada
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33
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Csilléry K, Buchmann N, Fady B. Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir ( Abies alba Mill.) populations. Evol Appl 2020; 13:2357-2376. [PMID: 33042220 PMCID: PMC7539328 DOI: 10.1111/eva.13029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a greenhouse experiment (N = 8,199) and on adult tress in situ (N = 315). In the greenhouse, we followed half-sib families for four growing seasons for growth and phenology traits, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ 13C, a proxy for water use efficiency, and genotyped at 357 SNP loci. SNP data was used to generate a null expectation for seedling trait divergence between populations in order to detect the signature of selection, and 31 environmental variables were used to identify the selective environment. We found that seedlings originating from populations with low soil water capacity grew more slowly, attained a smaller stature, and resisted water stress for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by their δ 13C. These results suggest a correlated evolution of the growth-drought tolerance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth-drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter- and intra-annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heterogeneous landscape, and can be used to inform assisted migration programs.
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Affiliation(s)
- Katalin Csilléry
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
- Biodiversity & Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Nina Buchmann
- Institute of Agricultural SciencesETH ZürichZürichSwitzerland
| | - Bruno Fady
- INRAEcology of Mediterranean Forests (URFM)UR629AvignonFrance
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34
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Du FK, Wang T, Wang Y, Ueno S, de Lafontaine G. Contrasted patterns of local adaptation to climate change across the range of an evergreen oak, Quercus aquifolioides. Evol Appl 2020; 13:2377-2391. [PMID: 33005228 PMCID: PMC7513717 DOI: 10.1111/eva.13030] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/02/2020] [Accepted: 05/09/2020] [Indexed: 12/27/2022] Open
Abstract
Long-lived tree species are genetically differentiated and locally adapted with respect to fitness-related traits, but the genetic basis of local adaptation remains largely unresolved. Recent advances in population genetics and landscape genomic analyses enable identification of putative adaptive loci and specific selective pressures acting on local adaptation. Here, we sampled 60 evergreen oak (Quercus aquifolioides) populations throughout the species' range and pool-sequenced 587 individuals at drought-stress candidate genes. We analyzed patterns of genetic diversity and differentiation for 381 single nucleotide polymorphisms (SNPs) from 65 candidate genes and eight microsatellites. Outlier loci were identified by genetic differentiation analysis and genome-environment associations. The response pattern of genetic variation to environmental gradient was assessed by linear isolation-by-distance/environment tests, redundancy analysis, and nonlinear methods. SNPs and microsatellites revealed two genetic lineages: Tibet and Hengduan Mountains-Western Sichuan Plateau (HDM-WSP), with reduced genetic diversity in Tibet lineage. More outlier loci were detected in HDM-WSP lineage than Tibet lineage. Among these, three SNPs in two genes responded to dry season precipitation in the HDM-WSP lineage but not in Tibet. By contrast, genetic variation in the Tibet lineage was related to geographic distance instead of the environment. Furthermore, risk of nonadaptedness (RONA) analyses suggested HDM-WSP lineage will have a better capacity to adapt in the predicted future climate compared with the Tibet lineage. We detected genetic imprints consistent with natural selection and molecular adaptation to drought on the Qinghai-Tibet Plateau (QTP) over a range of long-lived and widely distributed oak species in a changing environment. Our results suggest that different within-species adaptation processes occur in species occurring in heterogeneous environments.
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Affiliation(s)
- Fang K. Du
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Tianrui Wang
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Yuyao Wang
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukubaJapan
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
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Napier JD, de Lafontaine G, Hu FS. Exploring genomic variation associated with drought stress in Picea mariana populations. Ecol Evol 2020; 10:9271-9282. [PMID: 32953060 PMCID: PMC7487243 DOI: 10.1002/ece3.6614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/01/2020] [Accepted: 07/08/2020] [Indexed: 01/05/2023] Open
Abstract
Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype-by-environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | - Guillaume de Lafontaine
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of GeologyUniversity of IllinoisUrbanaILUSA
- Department of BiologyWashington UniversitySt. LouisMOUSA
- Department of Earth and Planetary SciencesWashington UniversitySt. LouisMOUSA
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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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37
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Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, Richter-Boix A, Laurila A, Höglund J. Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans. BMC Genet 2020; 21:38. [PMID: 32228443 PMCID: PMC7106915 DOI: 10.1186/s12863-020-00839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. RESULTS We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. CONCLUSION Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.,Centre for Paleogenetics Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Tom Van der Valk
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Alex Richter-Boix
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
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Species delimitation in the African tree genus Lophira (Ochnaceae) reveals cryptic genetic variation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01265-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Napier JD, Fernandez MC, de Lafontaine G, Hu FS. Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska. Ecol Evol 2020; 10:1692-1702. [PMID: 32076544 PMCID: PMC7029070 DOI: 10.1002/ece3.6031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 01/06/2020] [Indexed: 01/07/2023] Open
Abstract
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | | | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of GeologyUniversity of IllinoisUrbanaILUSA
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Napier JD, de Lafontaine G, Chipman ML. The Evolution of Paleoecology. Trends Ecol Evol 2020; 35:293-295. [PMID: 31959418 DOI: 10.1016/j.tree.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
While the interplay between migration and adaptation dictates species response to climate change, technological limitations have obfuscated explicit tests on past adaptive responses. However, a surge in technology-driven advances in paleoecological methods coincides with breakthroughs in processing ancient DNA, providing the first opportunity to assess adaptation to past climate shifts.
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Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern Flora, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Melissa L Chipman
- Department of Earth Sciences, Syracuse University, Syracuse, NY 13244, USA
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Mayol M, Riba M, Cavers S, Grivet D, Vincenot L, Cattonaro F, Vendramin GG, González‐Martínez SC. A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in Taxus baccata L. Evol Appl 2020; 13:143-160. [PMID: 31892949 PMCID: PMC6935595 DOI: 10.1111/eva.12838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
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Affiliation(s)
| | - Miquel Riba
- CREAFCerdanyola del VallèsSpain
- Univ. Autònoma BarcelonaCerdanyola del VallèsSpain
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research CentreINIA‐CIFORMadridSpain
- Sustainable Forest Management Research Institute, INIA‐University of ValladolidMadridSpain
| | | | | | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources, Division of FlorenceNational Research CouncilSesto FiorentinoItaly
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Walas Ł, Ganatsas P, Iszkuło G, Thomas PA, Dering M. Spatial genetic structure and diversity of natural populations of Aesculus hippocastanum L. in Greece. PLoS One 2019; 14:e0226225. [PMID: 31826015 PMCID: PMC6905551 DOI: 10.1371/journal.pone.0226225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/21/2019] [Indexed: 11/18/2022] Open
Abstract
Horse-chestnut (Aesculus hippocastanum L.) is an endemic and relict species from the Mediterranean biodiversity hotspot and a popular ornamental tree. Knowledge about the evolutionary history of this species remains scarce. Here, we ask what historical and ecological factors shaped the pattern of genetic diversity and differentiation of this species. We genotyped 717 individuals from nine natural populations using microsatellite markers. The influence of distance, topography and habitat variables on spatial genetic structure was tested within the approaches of isolation-by-distance and isolation-by-ecology. Species niche modeling was used to project the species theoretical range through time and space. The species showed high genetic diversity and moderate differentiation for which topography, progressive range contraction through the species’ history and long-term persistence in stable climatic refugia are likely responsible. A strong geographic component was revealed among five genetic clusters that are connected with very limited gene flow. The environmental variables were a significant factor in the spatial genetic structure. Modeling results indicated that future reduction of the species range may affect its survival. The possible impact of climate changes and high need of in situ conservation are discussed.
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Affiliation(s)
- Łukasz Walas
- Institute of Dendrology, Polish Academy of Sciences, Parkowa, Kórnik, Poland
- * E-mail:
| | - Petros Ganatsas
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Silviculture, Thessaloniki, Greece
| | - Grzegorz Iszkuło
- Institute of Dendrology, Polish Academy of Sciences, Parkowa, Kórnik, Poland
- Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana, Zielona Góra, Poland
| | - Peter A. Thomas
- School of Biological Sciences, Keele University, Staffordshire, United Kingdom
- Harvard Forest, Harvard University, Petersham, MA, United States of America
| | - Monika Dering
- Institute of Dendrology, Polish Academy of Sciences, Parkowa, Kórnik, Poland
- Faculty of Forestry, Poznań University of Life Sciences, Wojska Polskiego, Poznań, Poland
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Baltar F, Bayer B, Bednarsek N, Deppeler S, Escribano R, Gonzalez CE, Hansman RL, Mishra RK, Moran MA, Repeta DJ, Robinson C, Sintes E, Tamburini C, Valentin LE, Herndl GJ. Towards Integrating Evolution, Metabolism, and Climate Change Studies of Marine Ecosystems. Trends Ecol Evol 2019; 34:1022-1033. [DOI: 10.1016/j.tree.2019.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022]
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Dapporto L, Cini A, Vodă R, Dincă V, Wiemers M, Menchetti M, Magini G, Talavera G, Shreeve T, Bonelli S, Casacci LP, Balletto E, Scalercio S, Vila R. Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies. Mol Ecol Resour 2019; 19:1623-1636. [DOI: 10.1111/1755-0998.13059] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Affiliation(s)
| | - Alessandro Cini
- Dipartimento di Biologia dell'Università di Firenze Firenze Italy
- Centre for Biodiversity and Environment Research University College London London UK
| | - Raluca Vodă
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Vlad Dincă
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Martin Wiemers
- Senckenberg Deutsches Entomologisches Institut Müncheberg Germany
- Department of Community Ecology UFZ – Helmholtz Centre for Environmental Research Halle Germany
| | - Mattia Menchetti
- Dipartimento di Biologia dell'Università di Firenze Firenze Italy
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Giulia Magini
- Dipartimento di Biologia dell'Università di Firenze Firenze Italy
| | - Gerard Talavera
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Tim Shreeve
- Faculty of Health and Life Sciences, Centre for Ecology, Environment and Conservation Oxford Brookes University Oxford UK
| | - Simona Bonelli
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Luca Pietro Casacci
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
- Museum and Institute of Zoology Polish Academy of Sciences Warsaw Poland
| | - Emilio Balletto
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Stefano Scalercio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria Centro di Ricerca Foreste e Legno Rende Italy
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
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Creyaufmüller FC, Chassignet I, Delb H, Dounavi A, Gailing O, Leinemann L, Kreuzwieser J, Teply-Szymanski J, Vornam B. Terpene Synthase Genes in Quercus robur - Gene Characterization, Expression and Resulting Terpenes Due to Cockchafer Feeding. FRONTIERS IN PLANT SCIENCE 2018; 9:1753. [PMID: 30559755 PMCID: PMC6287202 DOI: 10.3389/fpls.2018.01753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
Root herbivory caused by larvae of the forest cockchafer (Melolontha hippocastani) enhances the impact of drought on trees, particularly in oak forest rejuvenations. In Germany, geographically distant oak stands show differences in infestation strength by the forest cockchafer. While in Southwestern Germany this insect causes severe damage, oak forests in northern Germany are rarely infested. It is known that root-released volatile organic compounds (VOCs) are perceived by soil herbivores, thus guiding the larvae toward the host roots. In this work, we exposed seedlings of two distant oak provenances to forest cockchafer larvae and studied their population genetic properties, their root-based VOC chemotypes, their attraction for larvae and terpene synthase gene expression. Based on nuclear and chloroplast marker analysis, we found both oak populations to be genetically highly variable while showing typical patterns of migration from different refugial regions. However, no clear association between genetic constitution of the different provenances and the abundance of cockchafer populations on site was observed. In contrast to observations in the field, bioassays revealed a preference of the larvae for the northeastern oak provenance. The behavior of larvae was most likely related to root-released volatile terpenes and benzenoids since their composition and quantity differed between oak populations. We assume repellent effects of these compounds because the populations attractive to insects showed low abundance of these compounds. Five different oak terpene synthase (TPS) genes were identified at the genomic level which can be responsible for biosynthesis of the released terpenes. TPS gene expression patterns in response to larval feeding revealed geographic variation rather than genotypic variation. Our results support the assumption that root-released VOC are influencing the perception of roots by herbivores.
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Affiliation(s)
| | - Isabelle Chassignet
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Horst Delb
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Aikaterini Dounavi
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
| | - Ludger Leinemann
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
| | - Jürgen Kreuzwieser
- Chair of Tree Physiology, Institute of Forest Science, University of Freiburg, Freiburg, Germany
| | - Julia Teply-Szymanski
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Barbara Vornam
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
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Strážnická M, Marková S, Searle JB, Kotlík P. Playing Hide-and-Seek in Beta-Globin Genes: Gene Conversion Transferring a Beneficial Mutation between Differentially Expressed Gene Duplicates. Genes (Basel) 2018; 9:genes9100492. [PMID: 30321987 PMCID: PMC6209878 DOI: 10.3390/genes9100492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that adaptation to diverse environments often involves selection on existing variation rather than new mutations. A previous study identified a nonsynonymous single nucleotide polymorphism (SNP) in exon 2 of two paralogous β-globin genes of the bank vole (Clethrionomys glareolus) in Britain in which the ancestral serine (Ser) and the derived cysteine (Cys) allele represent geographically partitioned functional variation affecting the erythrocyte antioxidative capacity. Here we studied the geographical pattern of the two-locus Ser/Cys polymorphism throughout Europe and tested for the geographic correlation between environmental variables and allele frequency, expected if the polymorphism was under spatially heterogeneous environment-related selection. Although bank vole population history clearly is important in shaping the dispersal of the oxidative stress protective Cys allele, analyses correcting for population structure suggest the Europe-wide pattern is affected by geographical variation in environmental conditions. The β-globin phenotype is encoded by the major paralog HBB-T1 but we found evidence of bidirectional gene conversion of exon 2 with the low-expression paralog HBB-T2. Our data support the model where gene conversion reshuffling genotypes between high- and low- expressed paralogs enables tuning of erythrocyte thiol levels, which may help maintain intracellular redox balance under fluctuating environmental conditions. Therefore, our study suggests a possible role for gene conversion between differentially expressed gene duplicates as a mechanism of physiological adaptation of populations to new or changing environments.
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Affiliation(s)
- Michaela Strážnická
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic.
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic.
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic.
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic.
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic.
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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