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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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2
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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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3
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Hopper KR. Reduced-representation libraries in insect genetics. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101084. [PMID: 37442341 DOI: 10.1016/j.cois.2023.101084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/04/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Genotyping-by-sequencing of reduced-representation libraries has ushered in an era where genome-wide data can be gotten for any species. Here, I review research on this topic during the last two years, report meta-analysis of the results, and discuss analysis methods and issues. Scanning the literature from 2021 to 2022 identified 21 papers, the majority of which were on population differences, including local adaptation and migration, but several papers were on genetic maps and their use in assembly scaffolding or analysis of quantitative trait loci, on the origin of incursions of pest insects, or on infection rates of a pathogen in a disease vector. The research reviewed includes 33 species from 25 families and 11 orders. Meta-analysis showed that less than 16%, and most often, less than 1% of the genome was implicated in local adaptation and that the number of adaptive loci correlated with genetic divergence among populations.
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Affiliation(s)
- Keith R Hopper
- Beneficial Insect Introductions Research Unit, ARS, USDA, Newark, DE, United States.
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4
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Dauphin B, Rellstab C, Wüest RO, Karger DN, Holderegger R, Gugerli F, Manel S. Re-thinking the environment in landscape genomics. Trends Ecol Evol 2023; 38:261-274. [PMID: 36402651 DOI: 10.1016/j.tree.2022.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022]
Abstract
Detecting the extrinsic selective pressures shaping genomic variation is critical for a better understanding of adaptation and for forecasting evolutionary responses of natural populations to changing environmental conditions. With increasing availability of geo-referenced environmental data, landscape genomics provides unprecedented insights into how genomic variation and underlying gene functions affect traits potentially under selection. Yet, the robustness of genotype-environment associations used in landscape genomics remains tempered due to various limitations, including the characteristics of environmental data used, sampling designs employed, and statistical frameworks applied. Here, we argue that using complementary or new environmental data sources and well-informed sampling designs may help improve the detection of selective pressures underlying patterns of local adaptation in various organisms and environments.
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Affiliation(s)
- Benjamin Dauphin
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland.
| | | | - Rafael O Wüest
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Dirk N Karger
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; Institute of Integrative Biology (IBZ), ETH, Zurich, 8092 Zurich, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Stéphanie Manel
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, 34000 Montpellier, France; Institut Universitaire de France, Paris, France
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5
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Martín-Blázquez R, Bakkali M, Ruiz-Estévez M, Garrido-Ramos MA. Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered Fern Vandenboschia speciosa. Genes (Basel) 2023; 14:genes14010166. [PMID: 36672907 PMCID: PMC9859580 DOI: 10.3390/genes14010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/10/2023] Open
Abstract
Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. In this study, we compare the transcriptomes of the sporophyte and the gametophyte of the endangered fern Vandenboschia speciosa. After Illumina sequencing and de novo transcriptome assembly of the gametophyte, annotation proved the existence of cross-species contamination in the gametophyte sample. Thus, we developed an in silico decontamination step for the gametophyte sequences. Once the quality check of the decontaminated reads passed, we produced a de novo assembly with the decontaminated gametophyte reads (with 43,139 contigs) and another combining the sporophyte and in silico decontaminated gametophyte reads (with 42,918 contigs). A comparison of the enriched GO terms from the top 1000 most expressed transcripts from both tissues showed that the gametophyte GO term set was enriched in sequences involved in development, response to stress, and plastid organization, while the sporophyte GO term set had a larger representation of more general metabolic functions. This study complements the available genomic resources on the life cycle of the endangered fern Vandenboschia speciosa.
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Affiliation(s)
- Rubén Martín-Blázquez
- Department of Evolutionary Ecology, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de la Cartuja, 41092 Sevilla, Spain
| | - Mohammed Bakkali
- Departamento de Genética, Universidad de Granada, 18071 Granada, Spain
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Harvey JA, Tougeron K, Gols R, Heinen R, Abarca M, Abram PK, Basset Y, Berg M, Boggs C, Brodeur J, Cardoso P, de Boer JG, De Snoo GR, Deacon C, Dell JE, Desneux N, Dillon ME, Duffy GA, Dyer LA, Ellers J, Espíndola A, Fordyce J, Forister ML, Fukushima C, Gage MJG, García‐Robledo C, Gely C, Gobbi M, Hallmann C, Hance T, Harte J, Hochkirch A, Hof C, Hoffmann AA, Kingsolver JG, Lamarre GPA, Laurance WF, Lavandero B, Leather SR, Lehmann P, Le Lann C, López‐Uribe MM, Ma C, Ma G, Moiroux J, Monticelli L, Nice C, Ode PJ, Pincebourde S, Ripple WJ, Rowe M, Samways MJ, Sentis A, Shah AA, Stork N, Terblanche JS, Thakur MP, Thomas MB, Tylianakis JM, Van Baaren J, Van de Pol M, Van der Putten WH, Van Dyck H, Verberk WCEP, Wagner DL, Weisser WW, Wetzel WC, Woods HA, Wyckhuys KAG, Chown SL. Scientists' warning on climate change and insects. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey A. Harvey
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Ecological Sciences Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Kévin Tougeron
- Earth and Life Institute, Ecology & Biodiversity Université catholique de Louvain Louvain‐la‐Neuve Belgium
- EDYSAN, UMR 7058, Université de Picardie Jules Verne, CNRS Amiens France
| | - Rieta Gols
- Laboratory of Entomology Wageningen University Wageningen The Netherlands
| | - Robin Heinen
- Department of Life Science Systems, School of Life Sciences Technical University of Munich, Terrestrial Ecology Research Group Freising Germany
| | - Mariana Abarca
- Department of Biological Sciences Smith College Northampton Massachusetts USA
| | - Paul K. Abram
- Agriculture and Agri‐Food Canada, Agassiz Research and Development Centre Agassiz British Columbia Canada
| | - Yves Basset
- Smithsonian Tropical Research Institute Panama City Republic of Panama
- Department of Ecology Institute of Entomology, Czech Academy of Sciences Ceske Budejovice Czech Republic
| | - Matty Berg
- Department of Ecological Sciences Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Carol Boggs
- School of the Earth, Ocean and Environment and Department of Biological Sciences University of South Carolina Columbia South Carolina USA
- Rocky Mountain Biological Laboratory Gothic Colorado USA
| | - Jacques Brodeur
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal Québec Canada
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus University of Helsinki Helsinki Finland
| | - Jetske G. de Boer
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Geert R. De Snoo
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Charl Deacon
- Department of Conservation Ecology and Entomology, Faculty of AgriSciences Stellenbosch University Stellenbosch South Africa
| | - Jane E. Dell
- Geosciences and Natural Resources Department Western Carolina University Cullowhee North Carolina USA
| | | | - Michael E. Dillon
- Department of Zoology and Physiology and Program in Ecology University of Wyoming Laramie Wyoming USA
| | - Grant A. Duffy
- School of Biological Sciences Monash University Melbourne Victoria Australia
- Department of Marine Science University of Otago Dunedin New Zealand
| | - Lee A. Dyer
- University of Nevada Reno – Ecology, Evolution and Conservation Biology Reno Nevada USA
| | - Jacintha Ellers
- Department of Ecological Sciences Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Anahí Espíndola
- Department of Entomology University of Maryland College Park Maryland USA
| | - James Fordyce
- Department of Ecology and Evolutionary Biology University of Tennessee, Knoxville Knoxville Tennessee USA
| | - Matthew L. Forister
- University of Nevada Reno – Ecology, Evolution and Conservation Biology Reno Nevada USA
| | - Caroline Fukushima
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus University of Helsinki Helsinki Finland
| | | | | | - Claire Gely
- Centre for Tropical Environmental and Sustainability Science, College of Science and Engineering James Cook University Cairns Queensland Australia
| | - Mauro Gobbi
- MUSE‐Science Museum, Research and Museum Collections Office Climate and Ecology Unit Trento Italy
| | - Caspar Hallmann
- Radboud Institute for Biological and Environmental Sciences Radboud University Nijmegen The Netherlands
| | - Thierry Hance
- Earth and Life Institute, Ecology & Biodiversity Université catholique de Louvain Louvain‐la‐Neuve Belgium
| | - John Harte
- Energy and Resources Group University of California Berkeley California USA
| | - Axel Hochkirch
- Department of Biogeography Trier University Trier Germany
- IUCN SSC Invertebrate Conservation Committee
| | - Christian Hof
- Department of Life Science Systems, School of Life Sciences Technical University of Munich, Terrestrial Ecology Research Group Freising Germany
| | - Ary A. Hoffmann
- Bio21 Institute, School of BioSciences University of Melbourne Melbourne Victoria Australia
| | - Joel G. Kingsolver
- Department of Biology University of North Carolina Chapel Hill North Carolina USA
| | - Greg P. A. Lamarre
- Smithsonian Tropical Research Institute Panama City Republic of Panama
- Department of Ecology Institute of Entomology, Czech Academy of Sciences Ceske Budejovice Czech Republic
| | - William F. Laurance
- Centre for Tropical Environmental and Sustainability Science, College of Science and Engineering James Cook University Cairns Queensland Australia
| | - Blas Lavandero
- Laboratorio de Control Biológico Universidad de Talca Talca Chile
| | - Simon R. Leather
- Center for Integrated Pest Management Harper Adams University Newport UK
| | - Philipp Lehmann
- Department of Zoology Stockholm University Stockholm Sweden
- Zoological Institute and Museum University of Greifswald Greifswald Germany
| | - Cécile Le Lann
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)] ‐ UMR 6553 Rennes France
| | | | - Chun‐Sen Ma
- Climate Change Biology Research Group, State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
| | - Gang Ma
- Climate Change Biology Research Group, State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
| | | | | | - Chris Nice
- Department of Biology Texas State University San Marcos Texas USA
| | - Paul J. Ode
- Department of Agricultural Biology Colorado State University Fort Collins Colorado USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado USA
| | - Sylvain Pincebourde
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS Université de Tours Tours France
| | - William J. Ripple
- Department of Forest Ecosystems and Society Oregon State University Oregon USA
| | - Melissah Rowe
- Netherlands Institute of Ecology (NIOO‐KNAW) Department of Animal Ecology Wageningen The Netherlands
| | - Michael J. Samways
- Department of Conservation Ecology and Entomology, Faculty of AgriSciences Stellenbosch University Stellenbosch South Africa
| | - Arnaud Sentis
- INRAE, Aix‐Marseille University, UMR RECOVER Aix‐en‐Provence France
| | - Alisha A. Shah
- W.K. Kellogg Biological Station, Department of Integrative Biology Michigan State University East Lansing Michigan USA
| | - Nigel Stork
- Centre for Planetary Health and Food Security, School of Environment and Science Griffith University Nathan Queensland Australia
| | - John S. Terblanche
- Department of Conservation Ecology and Entomology, Faculty of AgriSciences Stellenbosch University Stellenbosch South Africa
| | - Madhav P. Thakur
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Matthew B. Thomas
- York Environmental Sustainability Institute and Department of Biology University of York York UK
| | - Jason M. Tylianakis
- Bioprotection Aotearoa, School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Joan Van Baaren
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)] ‐ UMR 6553 Rennes France
| | - Martijn Van de Pol
- Netherlands Institute of Ecology (NIOO‐KNAW) Department of Animal Ecology Wageningen The Netherlands
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Wim H. Van der Putten
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Hans Van Dyck
- Earth and Life Institute, Ecology & Biodiversity Université catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | - David L. Wagner
- Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
| | - Wolfgang W. Weisser
- Department of Life Science Systems, School of Life Sciences Technical University of Munich, Terrestrial Ecology Research Group Freising Germany
| | - William C. Wetzel
- Department of Entomology, Department of Integrative Biology, and Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
| | - H. Arthur Woods
- Division of Biological Sciences University of Montana Missoula Montana USA
| | - Kris A. G. Wyckhuys
- Chrysalis Consulting Hanoi Vietnam
- China Academy of Agricultural Sciences Beijing China
| | - Steven L. Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences Monash University Melbourne Victoria Australia
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Malison RL, Hand BK, Winter E, Giersch JJ, Amish SJ, Whited D, Stanford JA, Luikart G. Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome. J Hered 2022; 113:453-471. [DOI: 10.1093/jhered/esac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO > 95% using “insecta_ob9” reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.
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Affiliation(s)
- Rachel L Malison
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
| | - Brian K Hand
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
| | - Emily Winter
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
| | - J Joseph Giersch
- US Geological Survey, Northern Rocky Mountain Science Center, Glacier National Park, West Glacier, Montana
| | - Stephen J Amish
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
- Conservation Genomics Group, Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Diane Whited
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
| | - Jack A Stanford
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
| | - Gordon Luikart
- The University of Montana, Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT
- Conservation Genomics Group, Division of Biological Sciences, University of Montana, Missoula, Montana
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Sheppard EC, Martin CA, Armstrong C, González-Quevedo C, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic associations with poxvirus across divergent island populations in Berthelot's pipit. Mol Ecol 2022; 31:3154-3173. [PMID: 35395699 PMCID: PMC9321574 DOI: 10.1111/mec.16461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/04/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot's pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses indicates that pathogen-mediated selection may play a role in shaping genomic variation among relatively recently colonised island bird populations and highlights the utility of genotype-environment associations for identifying candidate genes potentially involved in host-pathogen interactions.
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Affiliation(s)
- Eleanor C Sheppard
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Claire Armstrong
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Catalina González-Quevedo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.,Grupo Ecología y Evolución de Vertebrados, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Campus of Mieres, Research Building, 5th Floor, c/ Gonzalo Gutiérrez Quirós, s/n, 33600 Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.,Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
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9
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Hays CG, Hanley TC, Hughes AR, Truskey SB, Zerebecki RA, Sotka EE. Local Adaptation in Marine Foundation Species at Microgeographic Scales. THE BIOLOGICAL BULLETIN 2021; 241:16-29. [PMID: 34436968 DOI: 10.1086/714821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AbstractNearshore foundation species in coastal and estuarine systems (e.g., salt marsh grasses, mangroves, seagrasses, corals) drive the ecological functions of ecosystems and entire biomes by creating physical structure that alters local abiotic conditions and influences species interactions and composition. The resilience of foundation species and the ecosystem functions they provide depends on their phenotypic and genetic responses to spatial and temporal shifts in environmental conditions. In this review, we explore what is known about the causes and consequences of adaptive genetic differentiation in marine foundation species over spatial scales shorter than dispersal capabilities (i.e., microgeographic scales). We describe the strength of coupling field and laboratory experiments with population genetic techniques to illuminate patterns of local adaptation, and we illustrate this approach by using several foundation species. Among the major themes that emerge from our review include (1) adaptive differentiation of marine foundation species repeatedly evolves along vertical (i.e., elevation or depth) gradients, and (2) mating system and phenology may facilitate this differentiation. Microgeographic adaptation is an understudied mechanism potentially underpinning the resilience of many sessile marine species, and this evolutionary mechanism likely has particularly important consequences for the ecosystem functions provided by foundation species.
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Cao LJ, Li BY, Chen JC, Zhu JY, Hoffmann AA, Wei SJ. Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness. Mol Ecol 2021; 30:4204-4219. [PMID: 34278603 DOI: 10.1111/mec.16055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Schmidt TL, Swan T, Chung J, Karl S, Demok S, Yang Q, Field MA, Muzari MO, Ehlers G, Brugh M, Bellwood R, Horne P, Burkot TR, Ritchie S, Hoffmann AA. Spatial population genomics of a recent mosquito invasion. Mol Ecol 2021; 30:1174-1189. [PMID: 33421231 DOI: 10.1111/mec.15792] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/20/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Population genomic approaches can characterize dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG) and four incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232-577. Close kin dyads revealed recent movement between islands 31-203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and nonadjacent islands. Private alleles and a co-ancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.
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Affiliation(s)
- Thomas L Schmidt
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Tom Swan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Jessica Chung
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.,Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
| | - Stephan Karl
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Samuel Demok
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Qiong Yang
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Mutizwa Odwell Muzari
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Gerhard Ehlers
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Mathew Brugh
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Rodney Bellwood
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Peter Horne
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Thomas R Burkot
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Scott Ritchie
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia.,Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
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