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Zimmerman SJ, Aldridge CL, Schroeder MA, Fike JA, Cornman RS, Oyler-McCance SJ. The potential influence of genome-wide adaptive divergence on conservation translocation outcome in an isolated greater sage-grouse population. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14254. [PMID: 38563102 DOI: 10.1111/cobi.14254] [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: 08/04/2023] [Revised: 12/20/2023] [Accepted: 01/20/2024] [Indexed: 04/04/2024]
Abstract
Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse (Centrocercus urophasianus) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity (HO = 0.65) was higher in the recipient population than predicted had no augmentation occurred (HO = 0.58) but less than what was predicted by our model (HO = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index (FST) (143 genes) or local environmental variables (97 and 157 genes for each genotype-environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.
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Affiliation(s)
- Shawna J Zimmerman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | | | - Jennifer A Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Robert Scott Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Sara J Oyler-McCance
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
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2
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Sandercock AM, Westbrook JW, Zhang Q, Holliday JA. A genome-guided strategy for climate resilience in American chestnut restoration populations. Proc Natl Acad Sci U S A 2024; 121:e2403505121. [PMID: 39012830 PMCID: PMC11287244 DOI: 10.1073/pnas.2403505121] [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: 02/19/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024] Open
Abstract
American chestnut (Castanea dentata) is a deciduous tree species of eastern North America that was decimated by the introduction of the chestnut blight fungus (Cryphonectria parasitica) in the early 20th century. Although millions of American chestnuts survive as root collar sprouts, these trees rarely reproduce. Thus, the species is considered functionally extinct. American chestnuts with improved blight resistance have been developed through interspecific hybridization followed by conspecific backcrossing, and by genetic engineering. Incorporating adaptive genomic diversity into these backcross families and transgenic lines is important for restoring the species across broad climatic gradients. To develop sampling recommendations for ex situ conservation of wild adaptive genetic variation, we coupled whole-genome resequencing of 384 stump sprouts with genotype-environment association analyses and found that the species range can be subdivided into three seed zones characterized by relatively homogeneous adaptive allele frequencies. We estimated that 21 to 29 trees per seed zone will need to be conserved to capture most extant adaptive diversity. We also resequenced the genomes of 269 backcross trees to understand the extent to which the breeding program has already captured wild adaptive diversity, and to estimate optimal reintroduction sites for specific families on the basis of their adaptive portfolio and future climate projections. Taken together, these results inform the development of an ex situ germplasm conservation and breeding plan to target blight-resistant breeding populations to specific environments and provides a blueprint for developing restoration plans for other imperiled tree species.
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Affiliation(s)
| | | | - Qian Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech,Blacksburg, VA24060
| | - Jason A. Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech,Blacksburg, VA24060
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3
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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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4
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Poulin R, Salloum PM, Bennett J. Evolution of parasites in the Anthropocene: new pressures, new adaptive directions. Biol Rev Camb Philos Soc 2024. [PMID: 38984760 DOI: 10.1111/brv.13118] [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: 01/23/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
The Anthropocene is seeing the human footprint rapidly spreading to all of Earth's ecosystems. The fast-changing biotic and abiotic conditions experienced by all organisms are exerting new and strong selective pressures, and there is a growing list of examples of human-induced evolution in response to anthropogenic impacts. No organism is exempt from these novel selective pressures. Here, we synthesise current knowledge on human-induced evolution in eukaryotic parasites of animals, and present a multidisciplinary framework for its study and monitoring. Parasites generally have short generation times and huge fecundity, features that predispose them for rapid evolution. We begin by reviewing evidence that parasites often have substantial standing genetic variation, and examples of their rapid evolution both under conditions of livestock production and in serial passage experiments. We then present a two-step conceptual overview of the causal chain linking anthropogenic impacts to parasite evolution. First, we review the major anthropogenic factors impacting parasites, and identify the selective pressures they exert on parasites through increased mortality of either infective stages or adult parasites, or through changes in host density, quality or immunity. Second, we discuss what new phenotypic traits are likely to be favoured by the new selective pressures resulting from altered parasite mortality or host changes; we focus mostly on parasite virulence and basic life-history traits, as these most directly influence the transmission success of parasites and the pathology they induce. To illustrate the kinds of evolutionary changes in parasites anticipated in the Anthropocene, we present a few scenarios, either already documented or hypothetical but plausible, involving parasite taxa in livestock, aquaculture and natural systems. Finally, we offer several approaches for investigations and real-time monitoring of rapid, human-induced evolution in parasites, ranging from controlled experiments to the use of state-of-the-art genomic tools. The implications of fast-evolving parasites in the Anthropocene for disease emergence and the dynamics of infections in domestic animals and wildlife are concerning. Broader recognition that it is not only the conditions for parasite transmission that are changing, but the parasites themselves, is needed to meet better the challenges ahead.
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Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Priscila M Salloum
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Jerusha Bennett
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, New Zealand
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5
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Pettersson ME, Quintela M, Besnier F, Deng Q, Berg F, Kvamme C, Bekkevold D, Mosbech MB, Bunikis I, Lille-Langøy R, Leonori I, Wallberg A, Glover KA, Andersson L. Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring. Genome Biol Evol 2024; 16:evae133. [PMID: 38918882 PMCID: PMC11226789 DOI: 10.1093/gbe/evae133] [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: 02/26/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.
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Affiliation(s)
- Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Qiaoling Deng
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Florian Berg
- Institute of Marine Research, 5817 Bergen, Norway
| | | | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | | | | | - Iole Leonori
- CNR IRBIM, Italian National Research Council, Institute for Marine Biological Resources and Biotechnology, 60125 Ancona, Italy
| | - Andreas Wallberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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6
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Guillaume AS, Leempoel K, Rogivue A, Gugerli F, Parisod C, Joost S. Integrating very high resolution environmental proxies in genotype-environment association studies. Evol Appl 2024; 17:e13737. [PMID: 38948540 PMCID: PMC11212006 DOI: 10.1111/eva.13737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/20/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype-environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant Arabis alpina L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.
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Affiliation(s)
- Annie S. Guillaume
- Geospatial Molecular Epidemiology Group (GEOME), Laboratory for Biological Geochemistry (LGB), Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Kevin Leempoel
- Geospatial Molecular Epidemiology Group (GEOME), Laboratory for Biological Geochemistry (LGB), Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Royal Botanic Gardens, KewRichmond, SurreyUK
| | - Aude Rogivue
- WSL Swiss Federal Research InstituteBirmensdorfSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research InstituteBirmensdorfSwitzerland
| | | | - Stéphane Joost
- Geospatial Molecular Epidemiology Group (GEOME), Laboratory for Biological Geochemistry (LGB), Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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7
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Veale A, Reudink MW, Burg TM. Neutral markers reveal complex population structure across the range of a widespread songbird. Ecol Evol 2024; 14:e11638. [PMID: 38979005 PMCID: PMC11228359 DOI: 10.1002/ece3.11638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/17/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.
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Affiliation(s)
- Aaron Veale
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Matthew W. Reudink
- Department of Biological SciencesThompson Rivers UniversityKamloopsBritish ColumbiaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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8
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Omondi EO, Lin CY, Huang SM, Liao CA, Lin YP, Oliva R, van Zonneveld M. Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants. Ecol Evol 2024; 14:e11662. [PMID: 38983700 PMCID: PMC11232056 DOI: 10.1002/ece3.11662] [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: 09/09/2023] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.
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Affiliation(s)
- Emmanuel O Omondi
- Genetic Resources and Seed Unit World Vegetable Center Tainan Taiwan
| | - Chen-Yu Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | | | - Cheng-An Liao
- Department of Horticulture National Taiwan University Taipei Taiwan
| | - Ya-Ping Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | - Ricardo Oliva
- Plant Pathology World Vegetable Center Tainan Taiwan
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9
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Graham BA, Hipfner JM, Wellband KW, Ito M, Burg TM. Genetic-environment associations explain genetic differentiation and variation between western and eastern North Pacific rhinoceros auklet ( Cerorhinca monocerata) breeding colonies. Ecol Evol 2024; 14:e11534. [PMID: 38994218 PMCID: PMC11237344 DOI: 10.1002/ece3.11534] [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: 09/23/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 07/13/2024] Open
Abstract
Animals are strongly connected to the environments they live in and may become adapted to local environments. Examining genetic-environment associations of key indicator species, like seabirds, provides greater insights into the forces that drive evolution in marine systems. Here we examined a RADseq dataset of 19,213 SNPs for 99 rhinoceros auklets (Cerorhinca monocerata) from five western Pacific and 10 eastern Pacific breeding colonies. We used partial redundancy analyses to identify candidate adaptive loci and to quantify the effects of environmental variation on population genetic structure. We identified 262 candidate adaptive loci, which accounted for 3.0% of the observed genetic variation among western Pacific and eastern Pacific breeding colonies. Genetic variation was more strongly associated with pH and maximum current velocity, than maximum sea surface temperature. Genetic-environment associations explain genetic differences between western and eastern Pacific populations; however, genetic variation within the western and eastern Pacific Ocean populations appears to follow a pattern of isolation-by-distance. This study represents a first to quantify the relationship between environmental and genetic variation for this widely distributed marine species and provides greater insights into the evolutionary forces that act on marine species.
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Affiliation(s)
- Brendan A Graham
- Department of Biological Sciences University of Lethbridge Lethbridge Alberta Canada
- Institute of Arctic Biology University of Alaska Fairbanks Fairbanks Alaska USA
| | - J Mark Hipfner
- Wildlife Research Division Environment and Climate Change Canada Delta British Columbia Canada
| | - Kyle W Wellband
- Fisheries and Oceans Canada West Vancouver British Columbia Canada
| | - Motohiro Ito
- Faculty of Life Sciences Toyo University Bunkyō-ku Japan
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge Alberta Canada
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Portnoy DS, O'Leary SJ, Fields AT, Hollenbeck CM, Grubbs RD, Peterson CT, Gardiner JM, Adams DH, Falterman B, Drymon JM, Higgs JM, Pulster EL, Wiley TR, Murawski SA. Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic. Ecol Evol 2024; 14:e11514. [PMID: 38859886 PMCID: PMC11163162 DOI: 10.1002/ece3.11514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.
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Affiliation(s)
- David S. Portnoy
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - Shannon J. O'Leary
- Department of Biological SciencesSaint Anselm CollegeManchesterNew HampshireUSA
| | - Andrew T. Fields
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - Christopher M. Hollenbeck
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - R. Dean Grubbs
- Florida State University Coastal and Marine LaboratorySt. TeresaFloridaUSA
| | | | | | - Douglas H. Adams
- Florida Fish and Wildlife Conservation CommissionFish and Wildlife Research Institute, Indian River Field LabMelbourneFloridaUSA
| | | | - J. Marcus Drymon
- Mississippi State University Coastal Research and Extension CenterBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Jeremy M. Higgs
- Center for Fisheries Research and DevelopmentThe University of Southern MississippiOcean SpringsMississippiUSA
| | - Erin L. Pulster
- U.S. Geological Survey, Columbia Environmental Research CenterColumbiaMissouriUSA
- College of Marine ScienceUniversity of South FloridaSt. PetersburgFloridaUSA
| | | | - Steven A. Murawski
- College of Marine ScienceUniversity of South FloridaSt. PetersburgFloridaUSA
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11
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Tsai WLE, Escalona M, Garrett KL, Terrill RS, Sahasrabudhe R, Nguyen O, Beraut E, Seligmann W, Fairbairn CW, Harrigan RJ, McCormack JE, Alfaro ME, Smith TB, Bay RA. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered 2024; 115:317-325. [PMID: 38401156 PMCID: PMC11081134 DOI: 10.1093/jhered/esae008] [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: 12/22/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
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Affiliation(s)
- Whitney L E Tsai
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Kimball L Garrett
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, United States
| | - Ryan S Terrill
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Ryan J Harrigan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - John E McCormack
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA 95616, United States
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Liu B, Li J, Peng Y, Zhang K, Liu Q, Jin X, Zheng S, Wang Y, Gong L, Liu L, Lü Z, Liu Y. Chromosome-level genome assembly and population genomic analysis reveal evolution and local adaptation in common hairfin anchovy (Setipinna tenuifilis). Mol Ecol 2024; 33:e17067. [PMID: 37434292 DOI: 10.1111/mec.17067] [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: 05/26/2022] [Revised: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Understanding the genetic structure and the factors associated with adaptive diversity has significant implications for the effective management of wild populations under threat from overfishing and climate change. The common hairfin anchovy (Setipinna tenuifilis) is an economically and ecologically important pelagic fish species, spanning a broad latitudinal gradient along marginal seas of the Northwest Pacific. In this study, we constructed the first reference genome of S. tenuifilis using PacBio long reads and high-resolution chromosome conformation capture (Hi-C) technology. The assembled genome was 798.38 Mb with a contig N50 of 1.43 Mb and a scaffold N50 of 32.42 Mb, which were anchored onto 24 pseudochromosomes. A total of 22,019 genes were functionally annotated, which accounted for 95.27% of the predicted protein-coding genes. Chromosomal collinearity analysis revealed chromosome fusion or fission events in Clupeiformes species. Three genetic groups of S. tenuifilis were revealed along the Chinese coast using restriction site-associated DNA sequencing (RADseq). We investigated the influence of four bioclimatic variables as potential drivers of adaptive divergence in S. tenuifilis, suggesting that these environmental variables, especially sea surface temperature, may play important roles as drivers of spatially varying selection for S. tenuifilis. We also identified candidate functional genes underlying adaptive mechanisms and ecological tradeoffs using redundancy analysis (RDA) and BayeScan analysis. In summary, this study sheds light on the evolution and spatial patterns of genetic variation of S. tenuifilis, providing a valuable genomic resource for further biological and genetic studies on this species and other closely related Clupeiformes.
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Affiliation(s)
- Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd., Wuhan, China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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13
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Dai JX, Cao LJ, Chen JC, Yang F, Shen XJ, Ma LJ, Hoffmann AA, Chen M, Wei SJ. Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm. Mol Ecol 2024; 33:e17038. [PMID: 37277936 DOI: 10.1111/mec.17038] [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: 12/30/2022] [Accepted: 05/24/2023] [Indexed: 06/07/2023]
Abstract
Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.
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Affiliation(s)
- Jin-Xu Dai
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Min Chen
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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14
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Bell KL, Noreuil A, Molloy EK, Fritz ML. Genetic and behavioral differences between above and below ground Culex pipiens bioforms. Heredity (Edinb) 2024; 132:221-231. [PMID: 38424351 PMCID: PMC11074123 DOI: 10.1038/s41437-024-00675-4] [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: 08/24/2022] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes.
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Affiliation(s)
- Katherine L Bell
- Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Anna Noreuil
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Erin K Molloy
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA.
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15
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Sjodin BMF, Schmidt DA, Galbreath KE, Russello MA. Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients. Sci Rep 2024; 14:8568. [PMID: 38609461 PMCID: PMC11014952 DOI: 10.1038/s41598-024-59157-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Danielle A Schmidt
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, 1401 Presque Isle Ave, Marquette, MI, 49855, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
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16
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Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor MI, Wong MC. Variation in genomic vulnerability to climate change across temperate populations of eelgrass ( Zostera marina). Evol Appl 2024; 17:e13671. [PMID: 38650965 PMCID: PMC11033490 DOI: 10.1111/eva.13671] [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: 01/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 04/25/2024] Open
Abstract
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole-genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterize population structure, gene flow and environmental associations of 23 eelgrass populations ranging from the Northeast United States to Atlantic, subarctic and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise F ST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be potentially more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Benedikte Vercaemer
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries CentreSt. John'sNewfoundland and LabradorCanada
| | - France Dufresne
- Département de BiologieUniversité du Québec à RimouskiRimouskiQuebecCanada
| | - Fanny Noisette
- Institut des Sciences de la mer, Université du Québec à RimouskiRimouskiQuebecCanada
| | - Mary I. O'Connor
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Melisa C. Wong
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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17
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Kebede FG, Derks MFL, Dessie T, Hanotte O, Barros CP, Crooijmans RPMA, Komen H, Bastiaansen JWM. Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens. BMC Genomics 2024; 25:284. [PMID: 38500079 PMCID: PMC10946127 DOI: 10.1186/s12864-024-10193-6] [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: 10/03/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.
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Affiliation(s)
- Fasil Getachew Kebede
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands.
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - Tadelle Dessie
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
- School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Carolina Pita Barros
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - Hans Komen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - John W M Bastiaansen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
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18
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Lecomte L, Árnyasi M, Ferchaud A, Kent M, Lien S, Stenløkk K, Sylvestre F, Bernatchez L, Mérot C. Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations. Evol Appl 2024; 17:e13653. [PMID: 38495945 PMCID: PMC10940791 DOI: 10.1111/eva.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/14/2023] [Accepted: 01/13/2024] [Indexed: 03/19/2024] Open
Abstract
Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F ST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.
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Affiliation(s)
- Laurie Lecomte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
- Present address:
Parks Canada, Office of the Chief Ecosystem ScientistQuébecQCCanada
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Kristina Stenløkk
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Florent Sylvestre
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Département de BiologieUniversité LavalQuébecCanada
- Present address:
UMR 6553 Ecobio, OSUR, CNRSUniversité de RennesRennesFrance
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19
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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20
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Rojas‐Cortés ÁP, Gasca‐Pineda J, González‐Rodríguez A, Ibarra‐Manríquez G. Genomic diversity and structure of a Neotropical microendemic fig tree. Ecol Evol 2024; 14:e11178. [PMID: 38505177 PMCID: PMC10948372 DOI: 10.1002/ece3.11178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
Genetic diversity is a key component of evolution, and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is Ficus (Moraceae). It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of Ficus species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of Ficus pringlei to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. Ficus pringlei populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (F ST = 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as F. pringlei.
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Affiliation(s)
- Ángela P. Rojas‐Cortés
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMichoacánMexico
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de México, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Jaime Gasca‐Pineda
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Antonio González‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMichoacánMexico
| | - Guillermo Ibarra‐Manríquez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMichoacánMexico
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21
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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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22
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Zhou Y, Song R, Nevo E, Fu X, Wang X, Wang Y, Wang C, Chen J, Sun G, Sun D, Ren X. Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169679. [PMID: 38163608 DOI: 10.1016/j.scitotenv.2023.169679] [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: 09/21/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.
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Affiliation(s)
- Yu Zhou
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruilian Song
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eviator Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
| | - Xiaoqin Fu
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengyang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junpeng Chen
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Dongfa Sun
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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23
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Nunez JCB, Lenhart BA, Bangerter A, Murray CS, Mazzeo GR, Yu Y, Nystrom TL, Tern C, Erickson PA, Bergland AO. A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics 2024; 226:iyad207. [PMID: 38051996 PMCID: PMC10847723 DOI: 10.1093/genetics/iyad207] [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: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions.
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Affiliation(s)
- Joaquin C B Nunez
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Benedict A Lenhart
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Alyssa Bangerter
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Connor S Murray
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Giovanni R Mazzeo
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Yang Yu
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Taylor L Nystrom
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Courtney Tern
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Priscilla A Erickson
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alan O Bergland
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
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24
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Peng Y, Liu Y, Li J, Zhang K, Jin X, Zheng S, Wang Y, Lü Z, Liu L, Gong L, Liu B. New perspectives on the genetic structure of dotted gizzard shad ( Konosirus punctatus) based on RAD-seq. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:50-67. [PMID: 38433959 PMCID: PMC10901767 DOI: 10.1007/s42995-024-00216-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
Abstract
To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. Konosirus punctatus, which is a commercial fish species inhabiting the Indo-west Pacific Ocean, has shown an obvious annual global capture and aquaculture production decline due to climate changes and human activities. In the present study, restriction-site associated DNA sequencing (RAD-seq) was used to describe its genome-wide single nucleotide polymorphisms panel (SNPs). Among 146 individuals collected at nine locations scattered in China, Korea and Japan, a set of 632,090 SNPs were identified. Population genetic analysis showed that K. punctatus individuals were divided into two significant genetic clusters. Meanwhile, potential genetic differentiation between northern and southern population of K. punctatus was found. Treemix results indicated that gene flow existed among sampling locations of K. punctatus, especially from southern Japan to others. Moreover, candidate genes associated with habitat adaptations of K. punctatus were identified, which are involved in diverse physiological processes of K. punctatus including growth and development (e.g., KIDINS220, PAN3), substance metabolism (e.g., PGM5) and immune response (e.g., VAV3, CCT7, HSPA12B). Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of K. punctatus, which is beneficial to establish the management and conservation units of K. punctatus, guiding the rational use of resources, with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00216-2.
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Affiliation(s)
- Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022 China
- National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 China
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25
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Friis G, Smith EG, Lovelock CE, Ortega A, Marshell A, Duarte CM, Burt JA. Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula. Mol Ecol 2024; 33:e17260. [PMID: 38197286 DOI: 10.1111/mec.17260] [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: 12/07/2022] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.
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Affiliation(s)
- Guillermo Friis
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Catherine E Lovelock
- School of Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John A Burt
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
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26
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Wang W, Huang J, Hu Y, Feng J, Gao D, Fang W, Xu M, Ma C, Fu Z, Chen Q, Liang X, Lu J. Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:60-73. [PMID: 38147145 DOI: 10.1007/s10126-023-10277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
Abstract
Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.
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Affiliation(s)
- Wenhao Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yan Hu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianxiang Feng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Dong Gao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Meng Xu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chunlei Ma
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhenqiang Fu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Qinglong Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xuanguang Liang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China.
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China.
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27
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Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
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Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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28
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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29
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Iwasa-Arai T, Siqueira SGL, Sobral-Souza T, Leite FPP, Andrade SCS. Continent-island boundary and environment-shaped evolution in the marine amphipod Ampithoe marcuzzii complex (Crustacea: Eumalacostraca: Ampithoidae). Sci Rep 2024; 14:608. [PMID: 38182880 PMCID: PMC10770051 DOI: 10.1038/s41598-023-51049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024] Open
Abstract
Marine amphipods are crustaceans that lack a larval phase and consequently have low dispersion rates. Despite that, these crustaceans present a remarkable ability to be transported by rafting on natural floating substrata, especially macroalgae, where they find shelter, food and a mating ground. The species Ampithoe marcuzzii is widely distributed throughout the western Atlantic Ocean. Here, it was used as a model to study seascape genomics and phylogeography in invertebrates with low dispersion capacities. We anticipated that the lineages would present isolation-by-distance patterns. However, surface currents and other abiotic variables could facilitate connectivity among distant sites. Based on mitochondrial and nuclear genes, SNPs, and environmental associations, we observed the presence of a species complex within A. marcuzzii, separating mainland and insular populations. Each species showed an independent evolutionary history, with a strong latitudinal population structure and evidence of isolation-by-distance and isolation-by-environment, characterizing the 'continent' species. Historical expansion and environmental variables were observed associated with the southeastern population, and ecological niche modeling corroborated the region as a paleorefuge. Conversely, populations from 'islands' presented complicated evolutionary histories, with closer localities genetically isolated and distant localities connected. These findings indicate that insular populations with low dispersion capacity might be more susceptible to spatial connectivity by floating substrata and to changes in surface currents. In contrast, mainland populations might be more vulnerable to local climate changes due to lack of gene flow.
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Affiliation(s)
- Tammy Iwasa-Arai
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Silvana G L Siqueira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Fosca P P Leite
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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30
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Kardum Hjort C, Paris JR, Smith HG, Dudaniec RY. Selection despite low genetic diversity and high gene flow in a rapid island invasion of the bumblebee, Bombus terrestris. Mol Ecol 2024; 33:e17212. [PMID: 37990959 DOI: 10.1111/mec.17212] [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: 07/21/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
Invasive species are predicted to adjust their morphological, physiological and life-history traits to adapt to their non-native environments. Although a loss of genetic variation during invasion may restrict local adaptation, introduced species often thrive in novel environments. Despite being founded by just a few individuals, Bombus terrestris (Hymenoptera: Apidae) has in less than 30 years successfully spread across the island of Tasmania (Australia), becoming abundant and competitive with native pollinators. We use RADseq to investigate what neutral and adaptive genetic processes associated with environmental and morphological variation allow B. terrestris to thrive as an invasive species in Tasmania. Given the widespread abundance of B. terrestris, we expected little genetic structure across Tasmania and weak signatures of environmental and morphological selection. We found high gene flow with low genetic diversity, although with significant isolation-by-distance and spatial variation in effective migration rates. Restricted migration was evident across the mid-central region of Tasmania, corresponding to higher elevations, pastural land, low wind speeds and low precipitation seasonality. Tajima's D indicated a recent population expansion extending from the south to the north of the island. Selection signatures were found for loci in relation to precipitation, wind speed and wing loading. Candidate loci were annotated to genes with functions related to cuticle water retention and insect flight muscle stability. Understanding how a genetically impoverished invasive bumblebee has rapidly adapted to a novel island environment provides further understanding about the evolutionary processes that determine successful insect invasions, and the potential for invasive hymenopteran pollinators to spread globally.
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Affiliation(s)
- Cecilia Kardum Hjort
- Department of Biology, Lund University, Lund, Sweden
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Josephine R Paris
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Henrik G Smith
- Department of Biology, Lund University, Lund, Sweden
- Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Rachael Y Dudaniec
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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31
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Cheek RG, McLaughlin JF, Gamboa MP, Marshall CA, Johnson BM, Silver DB, Mauro AA, Ghalambor CK. A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years. Evol Appl 2024; 17:e13637. [PMID: 38283609 PMCID: PMC10818135 DOI: 10.1111/eva.13637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/17/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.
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Affiliation(s)
- Rebecca G. Cheek
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Jessica F. McLaughlin
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Maybellene P. Gamboa
- Department of Organismal Biology and EcologyColorado CollegeColorado SpringsColoradoUSA
| | - Craig A. Marshall
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Council on Science and TechnologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Brett M. Johnson
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Douglas B. Silver
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Alexander A. Mauro
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Cameron K. Ghalambor
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
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32
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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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Xiang X, Zhou X, Zi H, Wei H, Cao D, Zhang Y, Zhang L, Hu J. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. HORTICULTURE RESEARCH 2024; 11:uhad255. [PMID: 38274646 PMCID: PMC10809908 DOI: 10.1093/hr/uhad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.
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Affiliation(s)
- Xiaodong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xinglu Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Hantian Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Demei Cao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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Noirmain F, Baray JL, Deguillaume L, Van Baelen J, Latour D. Exploring the size-dependent dynamics of photosynthetic cells in rainwater: The influence of atmospheric variables and rain characteristics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167746. [PMID: 37827319 DOI: 10.1016/j.scitotenv.2023.167746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
The presence of microalgae in the atmosphere raises health and environmental concerns. Despite recent scientific advances, our knowledge of the origins and dynamics of photosynthetic cells in relation to atmospheric processes is limited due to a lack of empirical data. To address this gap, we conducted a one-year survey, collecting and analyzing rainwater samples. This study proposes to investigate the temporal dynamics of photosynthetic cells based on their size in combination with a unique dataset of variables of interest: type of rain and its characteristics, local meteorology, concentrations of inorganic chemical species, and long-range air mass transport. The analysis of the biochemical composition of rainwater, along with its correlation with the origin of air masses using ions as tracers, provides evidence of the long-range transport of photosynthetic cells. Additionally, our study reveals distinct removal mechanisms from the atmosphere for photosynthetic cells depending on their size. Our results suggest that convective events with high-intensity rainfall led to the efficient removal of medium-sized photosynthetic cells (4-15 μm) from the atmosphere. However, removal mechanisms for small (<4 μm) and large-sized cells (>15 μm) are not influenced by microphysical rainfall characteristics and seem to be governed by different atmospheric processes: dry deposition is proposed to be a significant mechanism for the removal of large-sized photosynthetic cells, while small-sized cells detected in rain are correlated with the horizontal wind speed and duration of rainfall, particularly during stratiform events. This implies that the removal of photosynthetic cells from the atmosphere is strongly influenced by environmental variables, which are expected to vary in response to global change. Therefore, it is crucial to enhance the monitoring of photosynthetic cells in relation to atmospheric processes and investigate the potential impact of the dissemination of genetic material from distant sources on recipient ecosystems.
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Affiliation(s)
- Fanny Noirmain
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome, Environnement (LMGE), UMR6023, Clermont-Ferrand, France.
| | - Jean-Luc Baray
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique (LaMP), UMR6016, Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont Ferrand (OPGC), UAR833, Clermont-Ferrand, France
| | - Laurent Deguillaume
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique (LaMP), UMR6016, Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont Ferrand (OPGC), UAR833, Clermont-Ferrand, France
| | - Joël Van Baelen
- Université de La Réunion, CNRS, Météo-France, Laboratoire de l'Atmosphère et des Cyclones (LACy), UMR8105, St Denis de la Réunion, France
| | - Delphine Latour
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome, Environnement (LMGE), UMR6023, Clermont-Ferrand, France
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35
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Miller CV, Bossu CM, Sarraco JF, Toews DPL, Rushing CS, Roberto-Charron A, Tremblay JA, Chandler RB, DeSaix MG, Fiss CJ, Larkin JL, Haché S, Nebel S, Ruegg KC. Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird. Mol Ecol 2024; 33:e17199. [PMID: 38018020 DOI: 10.1111/mec.17199] [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: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
Abstract
Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for CU identification in the Canada Warbler (Cardellina canadensis), a migratory bird species of conservation concern, and then integrate demographic modelling and genomic offset to guide conservation decisions. We find that patterns of whole genome genetic variation in this highly mobile species are primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two evolutionarily significant units (ESU), and three putative adaptive units (AUs) in the South, East, and Northwest. Quantification of genomic offset, a metric of genetic changes necessary to maintain current gene-environment relationships, revealed significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and future regional threats that can be used to inform management strategies for a highly mobile species in a rapidly changing world.
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Affiliation(s)
- Caitlin V Miller
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - James F Sarraco
- The Institute for Bird Populations, Petaluma, California, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Clark S Rushing
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | | | - Junior A Tremblay
- Wildlife Research Division, Environment and Climate Change Canada, Québec, Quebec, Canada
| | - Richard B Chandler
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | - Matthew G DeSaix
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Cameron J Fiss
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Jeff L Larkin
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Samuel Haché
- Canadian Wildlife Service, Environment Climate Change Canada, Yellowknife, Northwest Territories, Canada
| | | | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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Hoste A, Capblancq T, Broquet T, Denoyelle L, Perrier C, Buzan E, Šprem N, Corlatti L, Crestanello B, Hauffe HC, Pellissier L, Yannic G. Projection of current and future distribution of adaptive genetic units in an alpine ungulate. Heredity (Edinb) 2024; 132:54-66. [PMID: 38082151 PMCID: PMC10798982 DOI: 10.1038/s41437-023-00661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/21/2024] Open
Abstract
Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.
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Affiliation(s)
- Amélie Hoste
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Thibaut Capblancq
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Thomas Broquet
- CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Charles Perrier
- UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000, Zagreb, Croatia
| | - Luca Corlatti
- Stelvio National Park - ERSAF Lombardia, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Barbara Crestanello
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Loïc Pellissier
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zrich, Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Glenn Yannic
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
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Gao Y, Dai D, Wang H, Wu W, Xiao P, Wu L, Wei X, Yin S. Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China. Ecol Evol 2024; 14:e10861. [PMID: 38264337 PMCID: PMC10805605 DOI: 10.1002/ece3.10861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024] Open
Abstract
The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site-associated DNA sequencing (RAD-seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east-west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome-environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Dongqin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Haibo Wang
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Weijia Wu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Penghui Xiao
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Lifang Wu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Xiaomei Wei
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Si Yin
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
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38
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Pyron RA, Kakkera A, Beamer DA, O'Connell KA. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype. Mol Ecol 2024; 33:e17219. [PMID: 38015012 DOI: 10.1111/mec.17219] [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: 08/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Anvith Kakkera
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University, Greenville, North Carolina, USA
| | - Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
- Deloitte Consulting LLP, Health and Data AI, Arlington, Virginia, USA
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39
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Barr K, Bossu CM, Bay RA, Anderson EC, Belthoff J, Trulio LA, Chromczak D, Wisinski CL, Smith TB, Ruegg KC. Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evol Appl 2023; 16:1889-1900. [PMID: 38143900 PMCID: PMC10739168 DOI: 10.1111/eva.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 12/26/2023] Open
Abstract
Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Christen M. Bossu
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCaliforniaUSA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Jim Belthoff
- Raptor Research Center and Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Lynne A. Trulio
- Department of Environmental StudiesSan José State UniversitySan JoseCaliforniaUSA
| | - Debra Chromczak
- Burrowing Owl Researcher & ConsultantRiegelsvillePennsylvaniaUSA
| | | | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Kristen C. Ruegg
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
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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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Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). ANNALS OF BOTANY 2023; 132:499-512. [PMID: 37478307 PMCID: PMC10666999 DOI: 10.1093/aob/mcad104] [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: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND AND AIMS New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. METHODS We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. KEY RESULTS Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. CONCLUSIONS We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.
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Affiliation(s)
- Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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Muniz AC, de Oliveira Buzatti RS, de Lemos-Filho JP, Heuertz M, Nazareno AG, Lovato MB. Genomic signatures of ecological divergence between savanna and forest populations of a Neotropical tree. ANNALS OF BOTANY 2023; 132:523-540. [PMID: 37642427 PMCID: PMC10667007 DOI: 10.1093/aob/mcad120] [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: 05/01/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS In eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata, one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest-Cerrado. METHODS The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double-digest restriction site-associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated. KEY RESULTS High divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction. CONCLUSIONS The high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | | | - José Pires de Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Myriam Heuertz
- Biogeco, INRAE, Univ. Bordeaux, 69 route d’Arcachon, 33610 Cestas, France
| | - Alison Gonçalves Nazareno
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
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Wu R, Qi J, Li W, Wang L, Shen Y, Liu J, Teng Y, Roos C, Li M. Landscape genomics analysis provides insights into future climate change-driven risk in rhesus macaque. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165746. [PMID: 37495138 DOI: 10.1016/j.scitotenv.2023.165746] [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: 02/27/2023] [Revised: 07/01/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]
Abstract
Climate change significantly affects the suitability of wildlife habitats. Thus, understanding how animals adapt ecologically and genetically to climate change is important for targeted species protection. Rhesus macaques (Macaca mulatta) are widely distributed and multi-climatically adapted primates. This study explored how rhesus macaques adapt to climate change by integrating ecological and genetic methods and applying species distribution models (SDMs) and a gradient forest (GF) model. The findings suggested that temperature seasonality primarily affects habitat suitability and indicated that climate change will have a dramatic impact on macaque populations in the future. We also applied genotype-environment association (GEA) analyses and selection signature analyses to identify genes associated with climate change and provide possible explanations for the adaptation of rhesus macaques to climatic environments. The population genomics analyses suggested that the Taihang population has the highest genomic vulnerability with inbreeding and low heterozygosity. Combined with the higher ecological vulnerability, additional conservation strategies are required for this population under higher risk of climate change. Our work measured the impact of climate change and enabled the identification of populations that exhibit high vulnerability to severe climate change. Such information is useful for selecting populations of rhesus macaques as subject of long-term monitoring or evolutionary rescue under future climate change.
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Affiliation(s)
- Ruifeng Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Teng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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Feng S, Xi E, Wan W, Ru D. Genomic signals of local adaptation in Picea crassifolia. BMC PLANT BIOLOGY 2023; 23:534. [PMID: 37919677 PMCID: PMC10623705 DOI: 10.1186/s12870-023-04539-7] [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: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. RESULTS Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. CONCLUSIONS Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky JR, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo VL, Lucas SM, Lazic D, Gailing O, Carlson J, Staton M. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (BETHESDA, MD.) 2023; 13:jkad209. [PMID: 37708394 PMCID: PMC10627279 DOI: 10.1093/g3journal/jkad209] [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: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.
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Affiliation(s)
- Beant Kapoor
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Tatyana Zhebentyayeva
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40506, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Kuelheim
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, MI 49931, USA
| | - Mark Coggeshall
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chris Heim
- Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Leites
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, USDA-FS, SRS-4160, Department of Ecology & Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Victoria L DeLeo
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Lucas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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Bazzicalupo E, Ratkiewicz M, Seryodkin IV, Okhlopkov I, Galsandorj N, Yarovenko YA, Ozolins J, Saveljev AP, Melovski D, Gavashelishvili A, Schmidt K, Godoy JA. Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore Lynx lynx (Linnaeus, 1758). Evol Appl 2023; 16:1773-1788. [PMID: 38029067 PMCID: PMC10681490 DOI: 10.1111/eva.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 12/01/2023] Open
Abstract
Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north-western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre-adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.
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Affiliation(s)
- Enrico Bazzicalupo
- Department of Ecology and EvolutionEstación Biológica de Doñana (CSIC)SevilleSpain
| | | | - Ivan V. Seryodkin
- Laboratory of Ecology and Conservation of AnimalsPacific Institute of Geography of Far East Branch of Russian Academy of SciencesVladivostokRussia
| | - Innokentiy Okhlopkov
- Institute for Biological Problems of CryolithozoneSiberian Branch of the Russian Academy of SciencesYakutskRussia
| | | | - Yuriy A. Yarovenko
- Pre‐Caspian Institute of Biological ResourcesDagestan Federal Scientific Centre of RASMakhachkalaRussia
| | - Janis Ozolins
- Department of Hunting and Wildlife ManagementLatvijas Valsts mežzinātnes institūts "Silava"SalaspilsLatvia
| | - Alexander P. Saveljev
- Department of Animal EcologyRussian Research Institute of Game Management and Fur FarmingKirovRussia
| | - Dime Melovski
- Macedonian Ecological Society (MES)SkopjeNorth Macedonia
| | | | | | - José A. Godoy
- Department of Ecology and EvolutionEstación Biológica de Doñana (CSIC)SevilleSpain
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Chambers EA, Bishop AP, Wang IJ. Individual-based landscape genomics for conservation: An analysis pipeline. Mol Ecol Resour 2023. [PMID: 37883295 DOI: 10.1111/1755-0998.13884] [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: 03/27/2023] [Revised: 08/18/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
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Affiliation(s)
- E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
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Diniz FDA, Moura JDO, Bajay MM, Branco LC, Bezerra RD, de Araújo AM. Capra hircus outliers markers in Brazil: Searching for genomic regions under the action of natural selection. Genet Mol Biol 2023; 46:e20230084. [PMID: 37882366 PMCID: PMC10594045 DOI: 10.1590/1678-4685-gmb-2023-0084] [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: 03/22/2023] [Accepted: 08/21/2023] [Indexed: 10/27/2023] Open
Abstract
Identifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers' genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil.
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Affiliation(s)
- Francisco de A. Diniz
- Universidade Federal do Piauí, Teresina, PI, Brazil
- Instituto Federal do Piauí, Teresina, PI, Brazil
| | | | - Miklos M. Bajay
- Universidade do Estado de Santa Catarina, Laguna, SC, Brazil
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Wang TR, Meng HH, Wang N, Zheng SS, Jiang Y, Lin DQ, Song YG, Kozlowski G. Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera. ANNALS OF BOTANY 2023; 132:241-254. [PMID: 37409981 PMCID: PMC10583204 DOI: 10.1093/aob/mcad083] [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: 05/16/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND AND AIMS Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios. METHODS We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios. KEY RESULTS We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations. CONCLUSIONS Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.
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Affiliation(s)
- Tian-Rui Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Nian Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, 271018, China
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yun Jiang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Duo-Qing Lin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi-Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, Fribourg, CH-1700, Switzerland
- Natural History Museum Fribourg, Fribourg, CH-1700, Switzerland
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Márquez-Corro JI, Martín-Bravo S, Blanco-Pastor JL, Luceño M, Escudero M. The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients. Mol Ecol 2023. [PMID: 37795678 DOI: 10.1111/mec.17156] [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: 06/13/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023]
Abstract
Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.
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Affiliation(s)
- José Ignacio Márquez-Corro
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Jodrell Laboratory, Department of Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, UK
| | - Santiago Martín-Bravo
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - José Luis Blanco-Pastor
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
- Departamento de Biología, IVAGRO, Universidad de Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Cádiz, Spain
| | - Modesto Luceño
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
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