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Tomizawa Y, Wali KH, Surti M, Suhail Y, Kshitiz, Hoshino K. Lightsheet microscopy integrates single-cell optical visco-elastography and fluorescence cytometry of 3D live tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.20.590392. [PMID: 38766194 PMCID: PMC11100606 DOI: 10.1101/2024.04.20.590392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Most common cytometry methods, including flow cytometry, observe suspended or fixed cells and cannot evaluate their structural roles in 3D tissues. However, cellular physical interactions are critical in physiological, developmental, and pathological processes. Here, we present a novel optical visco-elastography that characterizes single-cellular physical interactions by applying in-situ micro-mechanical perturbation to live microtissues under 3D lightsheet microscopy. The 4D digital image correlation (DIC) analysis of ~20,000 nodes tracked the compressive deformation of 3D tissues containing ~500 cells. The computational 3D image segmentation allowed cell-by-cell qualitative observation and statistical analysis, directly correlating multi-channel fluorescence and viscoelasticity. To represent epithelia-stroma interactions, we used a 3D organoid model of maternal-fetal interface and visualized solid-like, well-aligned displacement and liquid-like random motion between individual cells. The statistical analysis through our unique cytometry confirmed that endometrial stromal fibroblasts stiffen in response to decidualization. Moreover, we demonstrated in the 3D model that interaction with placental extravillous trophoblasts partially reverses the attained stiffness, which was supported by the gene expression analysis. Placentation shares critical cellular and molecular significance with various fundamental biological events such as cancer metastasis, wound healing, and gastrulation. Our analysis confirmed existing beliefs and discovered new insights, proving the broad applicability of our method.
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Affiliation(s)
- Yuji Tomizawa
- Department of Biomedical Engineering, University of Connecticut, CT
| | - Khadija H Wali
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT
| | - Manav Surti
- Department of Biomedical Engineering, University of Connecticut, CT
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, CT
- Systems Biology Institute, Yale University, West Haven, CT
| | - Kazunori Hoshino
- Department of Biomedical Engineering, University of Connecticut, CT
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2
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Boyle JH, Strickler S, Twyford AD, Ricono A, Powell A, Zhang J, Xu H, Smith R, Dalgleish HJ, Jander G, Agrawal AA, Puzey JR. Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years. Curr Biol 2023; 33:3702-3710.e5. [PMID: 37607548 DOI: 10.1016/j.cub.2023.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/13/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023]
Abstract
In intimate ecological interactions, the interdependency of species may result in correlated demographic histories. For species of conservation concern, understanding the long-term dynamics of such interactions may shed light on the drivers of population decline. Here, we address the demographic history of the monarch butterfly, Danaus plexippus, and its dominant host plant, the common milkweed Asclepias syriaca (A. syriaca), using broad-scale sampling and genomic inference. Because genetic resources for milkweed have lagged behind those for monarchs, we first release a chromosome-level genome assembly and annotation for common milkweed. Next, we show that despite its enormous geographic range across eastern North America, A. syriaca is best characterized as a single, roughly panmictic population. Using approximate Bayesian computation with random forests (ABC-RF), a machine learning method for reconstructing demographic histories, we show that both monarchs and milkweed experienced population expansion during the most recent recession of North American glaciers 10,000-20,000 years ago. Our data also identify concurrent population expansions in both species during the large-scale clearing of eastern forests (∼200 years ago). Finally, we find no evidence that either species experienced a reduction in effective population size over the past 75 years. Thus, the well-documented decline of monarch abundance over the past 40 years is not visible in our genomic dataset, reflecting a possible mismatch of the overwintering census population to effective population size in this species.
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Affiliation(s)
- John H Boyle
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA; Biology Department, University of Mary, 7500 University Dr., Bismarck, ND 58504, USA
| | - Susan Strickler
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, IL 60022, USA; Northwestern University, Plant Biology and Conservation Program, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - Alex D Twyford
- Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Rd., Edinburgh EH9 3FL, UK; Royal Botanic Garden Edinburgh, Edinburgh EH3 5NZ, UK
| | - Angela Ricono
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Adrian Powell
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Jing Zhang
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Hongxing Xu
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; College of Life Sciences, Shaanxi Normal University, South Chang'an Rd., Xi'an 710062, China
| | - Ronald Smith
- Data Science Program, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Harmony J Dalgleish
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Joshua R Puzey
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA.
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3
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McDonald LM, Scharnagl A, Turcu AK, Patterson CM, Kooyers NJ. Demographic consequences of an extreme heat wave are mitigated by spatial heterogeneity in an annual monkeyflower. Ecol Evol 2023; 13:e10397. [PMID: 37575594 PMCID: PMC10412438 DOI: 10.1002/ece3.10397] [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: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023] Open
Abstract
Heat waves are becoming more frequent and intense with climate change, but the demographic and evolutionary consequences of heat waves are rarely investigated in herbaceous plant species. We examine the consequences of a short but extreme heat wave in Oregon populations of the common yellow monkeyflower (Mimulus guttatus) by leveraging a common garden experiment planted with range-wide populations and observational studies of 11 local populations. In the common garden, 89% of seedlings died during the heat wave including >96% of seedlings from geographically local populations. Some populations from hotter and drier environments had higher fitness, however, others from comparable environments performed poorly. Observational studies of local natural populations drastically differed in the consequences of the heat wave-one population was completely extirpated and nearly half had a >50% decrease in fitness. However, a few populations had greater fitness during the heat wave year. Differences in mortality corresponded to the impact of the heat wave on soil moisture-retention of soil moisture throughout the heat wave led to greater survivorship. Our results suggest that not all populations experience the same intensity or degree of mortality during extreme events and such heterogeneity could be important for genetic rescue or to facilitate the distribution of adaptive variants throughout the region.
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Affiliation(s)
| | - Anna Scharnagl
- Department of BiologyUniversity of LouisianaLafayetteLouisianaUSA
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Andrea K. Turcu
- Department of BiologyUniversity of LouisianaLafayetteLouisianaUSA
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Irimia RE, Montesinos D, Chaturvedi A, Sanders I, Hierro JL, Sotes G, Cavieres LA, Eren Ö, Lortie CJ, French K, Brennan AC. Trait evolution during a rapid global weed invasion despite little genetic differentiation. Evol Appl 2023; 16:997-1011. [PMID: 37216028 PMCID: PMC10197227 DOI: 10.1111/eva.13548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 05/24/2023] Open
Abstract
Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (F ST), and comparing it with phenotypic differentiation (P ST), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non-native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non-native ranges. The native versus invasive P ST-F ST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C. solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non-native populations.
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Affiliation(s)
- Ramona E. Irimia
- Centre for Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraPortugal
- Plant Evolutionary Ecology, Institute of Evolution and EcologyUniversity of TübingenTübingenGermany
| | - Daniel Montesinos
- Centre for Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraPortugal
- Australian Tropical HerbariumJames Cook UniversityQueenslandCairnsAustralia
| | - Anurag Chaturvedi
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Ian Sanders
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - José L. Hierro
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, UNLPamSanta RosaArgentina
| | - Gastón Sotes
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
| | - Lohengrin A. Cavieres
- Departamento de Botánica, Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Instituto de Ecología y Biodiversidad (IEB)SantiagoChile
| | - Özkan Eren
- Aydın Adnan Menderes Üniversitesi, Biyoloji Bölümü, Fen‐Edebiyat FakültesiAydınTurkey
| | - Christopher J. Lortie
- Department of BiologyYork UniversityOntarioTorontoCanada
- The National Center for Ecological Analysis and Synthesis (NCEAS), UCSBCaliforniaUSA
| | - Kristine French
- School of Earth, Atmospheric and Life SciencesUniversity of WollongongNew South WalesWollongongAustralia
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5
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Li Y, Chen J, Wang S, Jiang K, Zhou J, Zhu R, Gao C, Bu W, Xue H. Out of East Asia: Early Warning of the Possible Invasion of the Important Bean Pest Stalk-Eyed Seed Bug Chauliops fallax (Heteroptera: Malcidae: Chauliopinae). INSECTS 2023; 14:insects14050433. [PMID: 37233061 DOI: 10.3390/insects14050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
The short stay at the beginning of the invasion process is a critical time for invasive species identification and preventing invasive species from developing a wider distribution and significant economic impact. The stalk-eyed seed bug Chauliops fallax is an important agricultural pest of soybean and was first reported to occur outside East Asia. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of C. fallax for the first time based on population genetic methods and ecological niche modelling. The results showed that four native East Asian genetic groups (EA, WE, TL, and XZ) were well supported, showing an east-west differentiation pattern consistent with the geographical characteristics of three-step landforms in China. Two main haplotypes existed: Hap1 might have experienced a rapid northwards expansion process after the LGM period, and Hap5 reflected local adaptation to the environment in southeastern China. The Kashmir sample was found to come from the recent invasion of populations in the coastal areas of southern China. Ecological niche modelling results suggested that North America has a high risk of invasion, which might pose a serious threat to local soybean production. In addition, with future global warming, the suitable habitat in Asia will move towards the higher latitude region and gradually deviate from the soybean planting area, which indicates the threat of C. fallax to soybean production in Asia will decrease in the future. The results could provide new insights into the monitoring and management of this agricultural pest in the early invasion stage.
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Affiliation(s)
- Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiayue Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Runqi Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Cuiqing Gao
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
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6
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Tremble K, Hoffman JI, Dentinger BTM. Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis. THE NEW PHYTOLOGIST 2023; 237:295-309. [PMID: 36200167 DOI: 10.1111/nph.18521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis, a globally distributed species complex with broad ecological amplitude. By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62-2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene-Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.
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Affiliation(s)
- Keaton Tremble
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Natural History Museum of Utah, Salt Lake City, UT, 84108, USA
| | - J I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, 33501, Germany
| | - Bryn T M Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Natural History Museum of Utah, Salt Lake City, UT, 84108, USA
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7
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Rotter MC, Christie K, Holeski LM. Climate and the biotic community structure plant resistance across biogeographic groups of yellow monkeyflower. Ecol Evol 2022; 12:e9520. [DOI: 10.1002/ece3.9520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Michael C. Rotter
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Department of Biology Utah Valley University Orem Utah USA
| | - Kyle Christie
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Department of Plant Biology Michigan State University East Lansing Michigan USA
| | - Liza M. Holeski
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
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8
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Exposito-Alonso M, Booker TR, Czech L, Gillespie L, Hateley S, Kyriazis CC, Lang PLM, Leventhal L, Nogues-Bravo D, Pagowski V, Ruffley M, Spence JP, Toro Arana SE, Weiß CL, Zess E. Genetic diversity loss in the Anthropocene. Science 2022; 377:1431-1435. [PMID: 36137047 DOI: 10.1126/science.abn5642] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Anthropogenic habitat loss and climate change are reducing species' geographic ranges, increasing extinction risk and losses of species' genetic diversity. Although preserving genetic diversity is key to maintaining species' adaptability, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. We introduce a mathematical framework that bridges biodiversity theory and population genetics to understand the loss of naturally occurring DNA mutations with decreasing habitat. By analyzing genomic variation of 10,095 georeferenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a mutations-area relationship power law with geographic area, which can predict genetic diversity loss from local population extinctions. We estimate that more than 10% of genetic diversity may already be lost for many threatened and nonthreatened species, surpassing the United Nations' post-2020 targets for genetic preservation.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Lauren Gillespie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | | | - Laura Leventhal
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Nogues-Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Megan Ruffley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Jeffrey P Spence
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sebastian E Toro Arana
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin Zess
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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9
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Barrett CF, Huebner CD, Bender ZA, Budinsky TA, Corbett CW, Latvis M, McKain MR, Motley M, Skibicki SV, Thixton HL, Santee MV, Cumberledge AN. Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum. AMERICAN JOURNAL OF BOTANY 2022; 109:689-705. [PMID: 35435240 PMCID: PMC9327524 DOI: 10.1002/ajb2.1852] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Digitized collections can help illuminate the mechanisms behind the establishment and spread of invasive plants. These databases provide a record of traits in space and time that allows for investigation of abiotic and biotic factors that influence invasive species. METHODS Over 1100 digitized herbarium records were examined to investigate the invasion history and trait variation of Microstegium vimineum. Presence-absence of awns was investigated to quantify geographic patterns of this polymorphic trait, which serves several functions in grasses, including diaspore burial and dispersal to germination sites. Floret traits were further quantified, and genomic analyses of contemporary samples were conducted to investigate the history of M. vimineum's introduction and spread into North America. RESULTS Herbarium records revealed similar patterns of awn polymorphism in native and invaded ranges of M. vimineum, with awned forms predominating at higher latitudes and awnless forms at lower latitudes. Herbarium records and genomic data suggested initial introduction and spread of the awnless form in the southeastern United States, followed by a putative secondary invasion and spread of the awned form from eastern Pennsylvania. Awned forms have longer florets, and floret size varies significantly with latitude. There is evidence of a transition zone with short-awned specimens at mid-latitudes. Genomic analyses revealed two distinct clusters corresponding to awnless and awned forms, with evidence of admixture. CONCLUSIONS Our results demonstrate the power of herbarium data to elucidate the invasion history of a problematic weed in North America and, together with genomic data, reveal a possible key trait in introduction success: presence or absence of an awn.
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Affiliation(s)
- Craig F. Barrett
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
| | - Cynthia D. Huebner
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
- USDA Forest Service Northern Research Station180 Canfield StreetMorgantownWest Virginia26505USA
- Division of Plant and Soil Sciences, 4100 Agricultural Sciences BuildingP.O. Box 6108MorgantownWest Virginia26506USA
| | - Zoe A. Bender
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
- Department of BiologyGettysburg College300 North Washington StreetGettysburgPennsylvania17325USA
| | - Trezalka A. Budinsky
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
- Department of Biological SciencesUniversity of Pittsburgh4249 Fifth AvenuePittsburghPennsylvania15260USA
| | - Cameron W. Corbett
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
| | - Maribeth Latvis
- Department of Natural Resource ManagementSouth Dakota State University, 1390 College Avenue, South Dakota State UniversityBrookingsSouth Dakota57007USA
| | - Michael R. McKain
- Department of Biological SciencesUniversity of Alabama300 Hackberry LaneTuscaloosaAlabama35487USA
| | - M'Kayla Motley
- Department of Biological SciencesUniversity of Alabama300 Hackberry LaneTuscaloosaAlabama35487USA
| | - Samuel V. Skibicki
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
| | - Hana L. Thixton
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
| | - Mathilda V. Santee
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
| | - Aubrey N. Cumberledge
- Department of BiologyWest Virginia University53 Campus DriveMorgantownWest Virginia26506USA
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10
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Eckert S, Herden J, Stift M, Durka W, van Kleunen M, Joshi J. Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.856453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.
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11
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Brazier T, Cherif E, Martin JF, Gilles A, Blanchet S, Zhao Y, Combe M, McCairns RJS, Gozlan RE. The influence of native populations’ genetic history on the reconstruction of invasion routes: the case of a highly invasive aquatic species. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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12
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Kolis KM, Berg CS, Nelson TC, Fishman L. Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers. Evolution 2022; 76:765-781. [PMID: 35266558 DOI: 10.1111/evo.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 01/21/2023]
Abstract
Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.
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Affiliation(s)
- Kory M Kolis
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: O'Connor Center for the Rocky Mountain West, University of Montana, Missoula, MT, 59812
| | - Colette S Berg
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: Embark Veterinary, Inc., Boston, Massachusetts, 02210
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
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13
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Querns A, Wooliver R, Vallejo‐Marín M, Sheth SN. The evolution of thermal performance in native and invasive populations of
Mimulus guttatus. Evol Lett 2022; 6:136-148. [PMID: 35386831 PMCID: PMC8967274 DOI: 10.1002/evl3.275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/22/2021] [Accepted: 01/18/2022] [Indexed: 11/11/2022] Open
Abstract
The rise of globalization has spread organisms beyond their natural range, allowing further opportunity for species to adapt to novel environments and potentially become invaders. Yet, the role of thermal niche evolution in promoting the success of invasive species remains poorly understood. Here, we use thermal performance curves (TPCs) to test hypotheses about thermal adaptation during the invasion process. First, we tested the hypothesis that if species largely conserve their thermal niche in the introduced range, invasive populations may not evolve distinct TPCs relative to native populations, against the alternative hypothesis that thermal niche and therefore TPC evolution has occurred in the invasive range. Second, we tested the hypothesis that clines of TPC parameters are shallower or absent in the invasive range, against the alternative hypothesis that with sufficient time, standing genetic variation, and temperature‐mediated selection, invasive populations would re‐establish clines found in the native range in response to temperature gradients. To test these hypotheses, we built TPCs for 18 native (United States) and 13 invasive (United Kingdom) populations of the yellow monkeyflower, Mimulus guttatus. We grew clones of multiple genotypes per population at six temperature regimes in growth chambers. We found that invasive populations have not evolved different thermal optima or performance breadths, providing evidence for evolutionary stasis of thermal performance between the native and invasive ranges after over 200 years post introduction. Thermal optimum increased with mean annual temperature in the native range, indicating some adaptive differentiation among native populations that was absent in the invasive range. Further, native and invasive populations did not exhibit adaptive clines in thermal performance breadth with latitude or temperature seasonality. These findings suggest that TPCs remained unaltered post invasion, and that invasion may proceed via broad thermal tolerance and establishment in already climatically suitable areas rather than rapid evolution upon introduction.
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Affiliation(s)
- Aleah Querns
- Department of Plant and Microbial Biology North Carolina State University Raleigh North Carolina 27695
- Division of Biology Kansas State University Manhattan Kansas 66506
| | - Rachel Wooliver
- Department of Plant and Microbial Biology North Carolina State University Raleigh North Carolina 27695
- Department of Biosystems Engineering and Soil Science University of Tennessee Knoxville Knoxville Tennessee 37996
| | - Mario Vallejo‐Marín
- Biological and Environmental Sciences University of Stirling Stirling FK9 4LA United Kingdom
| | - Seema Nayan Sheth
- Department of Plant and Microbial Biology North Carolina State University Raleigh North Carolina 27695
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14
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North HL, McGaughran A, Jiggins CD. Insights into invasive species from whole-genome resequencing. Mol Ecol 2021; 30:6289-6308. [PMID: 34041794 DOI: 10.1111/mec.15999] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.
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Affiliation(s)
- Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
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15
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Sutherland BL, Barrett CF, Beck JB, Latvis M, McKain MR, Sigel EM, Kooyers NJ. Botany is the root and the future of invasion biology. AMERICAN JOURNAL OF BOTANY 2021; 108:549-552. [PMID: 33893635 DOI: 10.1002/ajb2.1642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Affiliation(s)
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - James B Beck
- Biological Sciences Department, Wichita State University, Wichita, KS, USA
| | - Maribeth Latvis
- Department of Natural Resources Management, South Dakota State University, Brookings, SD, USA
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Erin M Sigel
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Nicholas J Kooyers
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
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