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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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2
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Steward RA, Pruisscher P, Roberts KT, Wheat CW. Genetic constraints in genes exhibiting splicing plasticity in facultative diapause. Heredity (Edinb) 2024; 132:142-155. [PMID: 38291272 PMCID: PMC10923799 DOI: 10.1038/s41437-024-00669-2] [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: 02/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.
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Affiliation(s)
- Rachel A Steward
- Zoology Department, Stockholm University, Stockholm, Sweden.
- Biology Department, Lund University, Lund, Sweden.
| | - Peter Pruisscher
- Zoology Department, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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3
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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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4
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Feng S, DeGrey SP, Guédot C, Schoville SD, Pool JE. Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547576. [PMID: 37461625 PMCID: PMC10349955 DOI: 10.1101/2023.07.03.547576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Biological invasions carry substantial practical and scientific importance, and represent natural evolutionary experiments on contemporary timescales. Here, we investigated genomic diversity and environmental adaptation of the crop pest Drosophila suzukii using whole-genome sequencing data and environmental metadata for 29 population samples from its native and invasive range. Through a multifaceted analysis of this population genomic data, we increase our understanding of the D. suzukii genome, its diversity and its evolution, and we identify an appropriate genotype-environment association pipeline for our data set. Using this approach, we detect genetic signals of local adaptation associated with nine distinct environmental factors related to altitude, wind speed, precipitation, temperature, and human land use. We uncover unique functional signatures for each environmental variable, such as a prevalence of cuticular genes associated with annual precipitation. We also infer biological commonalities in the adaptation to diverse selective pressures, particularly in terms of the apparent contribution of nervous system evolution to enriched processes (ranging from neuron development to circadian behavior) and to top genes associated with all nine environmental variables. Our findings therefore depict a finer-scale adaptive landscape underlying the rapid invasion success of this agronomically important species.
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Affiliation(s)
- Siyuan Feng
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel P. DeGrey
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christelle Guédot
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
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Matthews AE, Boves TJ, Percy KL, Schelsky WM, Wijeratne AJ. Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution. Life (Basel) 2023; 13:2054. [PMID: 37895435 PMCID: PMC10608719 DOI: 10.3390/life13102054] [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: 06/29/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.
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Affiliation(s)
- Alix E. Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR 72401, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
| | - Than J. Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
| | - Katie L. Percy
- Audubon Delta, National Audubon Society, Baton Rouge, LA 70808, USA;
- United States Department of Agriculture, Natural Resources Conservation Service, Addis, LA 70710, USA
| | - Wendy M. Schelsky
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, Champaign, IL 61801, USA;
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Urbana-Champaign, Champaign, IL 61820, USA
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
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6
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deMayo JA, Brennan RS, Pespeni MH, Finiguerra M, Norton L, Park G, Baumann H, Dam HG. Simultaneous warming and acidification limit population fitness and reveal phenotype costs for a marine copepod. Proc Biol Sci 2023; 290:20231033. [PMID: 37670582 PMCID: PMC10510449 DOI: 10.1098/rspb.2023.1033] [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: 08/02/2022] [Accepted: 07/25/2023] [Indexed: 09/07/2023] Open
Abstract
Phenotypic plasticity and evolutionary adaptation allow populations to cope with global change, but limits and costs to adaptation under multiple stressors are insufficiently understood. We reared a foundational copepod species, Acartia hudsonica, under ambient (AM), ocean warming (OW), ocean acidification (OA), and combined ocean warming and acidification (OWA) conditions for 11 generations (approx. 1 year) and measured population fitness (net reproductive rate) derived from six life-history traits (egg production, hatching success, survival, development time, body size and sex ratio). Copepods under OW and OWA exhibited an initial approximately 40% fitness decline relative to AM, but fully recovered within four generations, consistent with an adaptive response and demonstrating synergy between stressors. At generation 11, however, fitness was approximately 24% lower for OWA compared with the AM lineage, consistent with the cost of producing OWA-adapted phenotypes. Fitness of the OWA lineage was not affected by reversal to AM or low food environments, indicating sustained phenotypic plasticity. These results mimic those of a congener, Acartia tonsa, while additionally suggesting that synergistic effects of simultaneous stressors exert costs that limit fitness recovery but can sustain plasticity. Thus, even when closely related species experience similar stressors, species-specific costs shape their unique adaptive responses.
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Affiliation(s)
- James A. deMayo
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Reid S. Brennan
- Department of Biology, University of Vermont, Burlington, VT, USA
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Melissa H. Pespeni
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Finiguerra
- Department of Ecology and Evolutionary Biology, University of Connecticut, Groton, CT, USA
| | - Lydia Norton
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Gihong Park
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Hannes Baumann
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Hans G. Dam
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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7
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Leiva C, Pérez-Portela R, Lemer S. Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO 2 seeps. Commun Biol 2023; 6:769. [PMID: 37481685 PMCID: PMC10363134 DOI: 10.1038/s42003-023-05103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023] Open
Abstract
Ocean acidification, caused by anthropogenic CO2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival.
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Affiliation(s)
- Carlos Leiva
- University of Guam Marine Laboratory, 303 University Drive, 96923, Mangilao, Guam, USA.
| | - Rocío Pérez-Portela
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sarah Lemer
- University of Guam Marine Laboratory, 303 University Drive, 96923, Mangilao, Guam, USA
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8
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Buswell VG, Ellis JS, Huml JV, Wragg D, Barnett MW, Brown A, Knight ME. When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera. INSECTS 2023; 14:insects14050421. [PMID: 37233049 DOI: 10.3390/insects14050421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.
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Affiliation(s)
- Victoria G Buswell
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Jonathan S Ellis
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - J Vanessa Huml
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Mark W Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Andrew Brown
- B4, Newton Farm Metherell, Cornwall, Callington PL17 8DQ, UK
| | - Mairi E Knight
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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9
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Osterman J, Hammenhag C, Ortiz R, Geleta M. Discovering candidate SNPs for resilience breeding of red clover. FRONTIERS IN PLANT SCIENCE 2022; 13:997860. [PMID: 36247534 PMCID: PMC9554550 DOI: 10.3389/fpls.2022.997860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 06/02/2023]
Abstract
Red clover is a highly valuable crop for the ruminant industry in the temperate regions worldwide. It also provides multiple environmental services, such as contribution to increased soil fertility and reduced soil erosion. This study used 661 single nucleotide polymorphism (SNP) markers via targeted sequencing using seqSNP, to describe genetic diversity and population structure in 382 red clover accessions. The accessions were selected from NordGen representing red clover germplasm from Norway, Sweden, Finland and Denmark as well as from Lantmännen, a Swedish seed company. Each accession was represented by 10 individuals, which was sequenced as a pool. The mean Nei's standard genetic distance between the accessions and genetic variation within accessions were 0.032 and 0.18, respectively. The majority of the accessions had negative Tajima's D, suggesting that they contain significant proportions of rare alleles. A pairwise FST revealed high genetic similarity between the different cultivated types, while the wild populations were divergent. Unlike wild populations, which exhibited genetic differentiation, there was no clear differentiation among all cultivated types. A principal coordinate analysis revealed that the first principal coordinate, distinguished most of the wild populations from the cultivated types, in agreement with the results obtained using a discriminant analysis of principal components and cluster analysis. Accessions of wild populations and landraces collected from southern and central Scandinavia showed a higher genetic similarity to Lantmännen accessios. It is therefore possible to link the diversity of the environments where wild populations were collected to the genetic diversity of the cultivated and wild gene pools. Additionally, least absolute shrinkage and selection operator (LASSO) models revealed associations between variation in temperature and precipitation and SNPs within genes controlling stomatal opening. Temperature was also related to kinase proteins, which are known to regulate plant response to temperature stress. Furthermore, the variation between wild populations and cultivars was correlated with SNPs within genes regulating root development. Overall, this study comprehensively investigated Nordic European red clover germplasm, and the results provide forage breeders with valuable information for further selection and development of red clover cultivars.
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10
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Weber JN, Steinel NC, Peng F, Shim KC, Lohman BK, Fuess LE, Subramanian S, Lisle SPD, Bolnick DI. Evolutionary gain and loss of a pathological immune response to parasitism. Science 2022; 377:1206-1211. [PMID: 36074841 PMCID: PMC9869647 DOI: 10.1126/science.abo3411] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Parasites impose fitness costs on their hosts. Biologists often assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests that selection may sometimes favor loss of resistance, which may result in alternative stable states where some populations are resistant and others are tolerant. Intraspecific variation in immune costs is rarely surveyed in a manner that tests evolutionary patterns, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes, they gained resistance to the freshwater-associated cestode Schistocephalus solidus. Extensive peritoneal fibrosis and inflammation are a commonly observed phenotype that contributes to suppression of cestode growth and viability but also imposes a substantial cost on fecundity. Combining genetic mapping and population genomics, we find that opposing selection generates immune system differences between tolerant and resistant populations, consistent with divergent optimization.
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Affiliation(s)
- Jesse N Weber
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Natalie C Steinel
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Foen Peng
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Kum Chuan Shim
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Brian K Lohman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Lauren E Fuess
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Swapna Subramanian
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Stephen P De Lisle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Mol Biol Evol 2021; 38:5782-5805. [PMID: 34469576 PMCID: PMC8662648 DOI: 10.1093/molbev/msab259] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
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Affiliation(s)
- Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of
Zürich, Switzerland
- Department of Cell & Developmental Biology, Center of Anatomy and Cell
Biology, Medical University of Vienna, Vienna, Austria
| | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Jesús Murga-Moreno
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Margot Paris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joseph Outten
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Courtney Tern
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment, University of Trento, San Michele all'
Adige, Italy
| | | | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of
Jyväskylä, Jyväskylä, Finland
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia,
Pavia, Italy
| | | | - Banu S Onder
- Department of Biology, Hacettepe University, Ankara, Turkey
| | | | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Division of Biological and Life Sciences, School of Arts and Sciences,
Ahmedabad University, Ahmedabad, India
| | - Emily L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Janelia Research Campus, Ashburn, VA, USA
| | - Mads F Schou
- Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Biology, Lund University, Lund, Sweden
| | - Thomas J S Merritt
- Department of Chemistry & Biochemistry, Laurentian
University, Sudbury, ON, Canada
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY,
USA
| | - Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Eliza Argyridou
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Fabian Staubach
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Yun Wang
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution,
University of Haifa, Haifa, Israel
| | - Svitlana V Serga
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge,
United Kingdom
| | - Kelly A Dyer
- Department of Genetics, University of Georgia, Athens, GA,
USA
| | | | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | | | | | - Mihailo Jelic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | | | | | | | - Aleksandra Patenkovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Katarina Eric
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Tanaskovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Anna Ullastres
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Lain Guio
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Sara Guirao-Rico
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Vivien Horváth
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Elena Pasyukova
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Vladimir E Alatortsev
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | | | - Iryna Kozeretska
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Oleksandr M Maistrenko
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- Structural and Computational Biology Unit, European Molecular Biology
Laboratory, Heidelberg, Germany
| | | | - Dmitry V Mukha
- Vavilov Institute of General Genetics, Russian Academy of
Sciences, Moscow, Russia
| | - Heather E Machado
- Department of Biology, Stanford University, Stanford, CA,
USA
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Keric Lamb
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Tânia Paulo
- Departamento de Biologia Animal, Instituto Gulbenkian de Ciência,
Oeiras, Portugal
| | - Leeban Yusuf
- Center for Biological Diversity, University of St. Andrews, St
Andrews, United Kingdom
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA,
USA
| | - Paul Schmidt
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Josefa Gonzalez
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
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