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Seeley MM, Stacy EA, Martin RE, Asner GP. Foliar functional and genetic variation in a keystone Hawaiian tree species estimated through spectroscopy. Oecologia 2023; 202:15-28. [PMID: 37171625 DOI: 10.1007/s00442-023-05374-1] [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: 10/12/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Imaging spectroscopy has the potential to map closely related plant taxa at landscape scales. Although spectral investigations at the leaf and canopy levels have revealed relationships between phylogeny and reflectance, understanding how spectra differ across, and are inherited from, genotypes of a single species has received less attention. We used a common-garden population of four varieties of the keystone canopy tree, Metrosideros polymorpha, from Hawaii Island and four F1-hybrid genotypes derived from controlled crosses to determine if reflectance spectra discriminate sympatric, conspecific varieties of this species and their hybrids. With a single exception, pairwise comparisons of leaf reflectance patterns successfully distinguished varieties of M. polymorpha on Hawaii Island as well as populations of the same variety from different islands. Further, spectral variability within a single variety from Hawaii Island and the older island of Oahu was greater than that observed among the four varieties on Hawaii Island. F1 hybrids most frequently displayed leaf spectral patterns intermediate to those of their parent taxa. Spectral reflectance patterns distinguished each of two of the hybrid genotypes from one of their parent varieties, indicating that classifying hybrids may be possible, particularly if sample sizes are increased. This work quantifies a baseline in spectral variability for an endemic Hawaiian tree species and advances the use of imaging spectroscopy in biodiversity studies at the genetic level.
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Affiliation(s)
- M M Seeley
- Center for Global Discovery and Conservation Science, Arizona State University, Hilo, HI, 96720, USA.
- School of Geographical Sciences and Urban Planning, Arizona State University, Tempe, AZ, 85281, USA.
| | - E A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, NV, 89154, USA
| | - R E Martin
- Center for Global Discovery and Conservation Science, Arizona State University, Hilo, HI, 96720, USA
- School of Geographical Sciences and Urban Planning, Arizona State University, Tempe, AZ, 85281, USA
| | - G P Asner
- Center for Global Discovery and Conservation Science, Arizona State University, Hilo, HI, 96720, USA
- School of Geographical Sciences and Urban Planning, Arizona State University, Tempe, AZ, 85281, USA
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Hadi M, Stacy EA. An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11518. [PMID: 37342165 PMCID: PMC10278935 DOI: 10.1002/aps3.11518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 06/22/2023]
Abstract
Premise The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse Metrosideros taxa representing a broad range of leaf toughness, pubescence, and secondary metabolites. Methods and Results We tested popular RNA isolation kits and protocols that were effective on other recalcitrant trees, including a broad range of optimization and purification steps. We optimized a protocol involving two silica-membrane column-based kits that yielded high-quantity RNA with an RNA integrity number >7 and without DNA contamination. All RNA samples were used successfully in a follow-on RNA-Seq experiment. Conclusions We present an optimized high-throughput RNA extraction protocol that yielded high-quality and high-quantity RNA from three contrasting leaf phenotypes within a hyperdiverse woody species complex.
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Affiliation(s)
- Maryam Hadi
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevada89154USA
| | - Elizabeth A. Stacy
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevada89154USA
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Sur GL, Zahn G, Stacy EA. Examination of host-taxon, environment, and distance effects on leaf fungal endophytes in the dominant woody genus, Metrosideros, on Oʻahu. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Choi JY, Dai X, Alam O, Peng JZ, Rughani P, Hickey S, Harrington E, Juul S, Ayroles JF, Purugganan MD, Stacy EA. Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands. Proc Natl Acad Sci U S A 2021; 118:e2023801118. [PMID: 34497122 PMCID: PMC8449318 DOI: 10.1073/pnas.2023801118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2021] [Indexed: 01/05/2023] Open
Abstract
Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003;
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Inc., New York, NY 10013
| | - Ornob Alam
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Julie Z Peng
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | | | - Scott Hickey
- Oxford Nanopore Technologies Inc., San Francisco, CA 94501
| | | | - Sissel Juul
- Oxford Nanopore Technologies Inc., New York, NY 10013
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89119;
- College of Agriculture, Forestry, and Natural Resource Management, University of Hawaii Hilo, Hilo, HI 96720
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Magota K, Sakaguchi S, Hirota SK, Tsunamoto Y, Suyama Y, Akai K, Setoguchi H. Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei. AMERICAN JOURNAL OF BOTANY 2021; 108:680-693. [PMID: 33881773 DOI: 10.1002/ajb2.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures. METHODS To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences. RESULTS We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation. CONCLUSIONS Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.
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Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| | - Shun K Hirota
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center, Forestry and Forest Products Research Institute, 92-25 Nabeyashiki, Shimo-kuriyagawa, Morioka, Iwate, 020-0123, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Kensei Akai
- International Center for Island Studies Amami Station, Kagoshima University, Naze-Minatomachi 15-1, Amami, Kagoshima, 894-0026, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
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Choi JY, Purugganan M, Stacy EA. Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island. Mol Biol Evol 2020; 37:695-710. [PMID: 31693149 PMCID: PMC7038655 DOI: 10.1093/molbev/msz259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Michael Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
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Gillespie RG, Bennett GM, De Meester L, Feder JL, Fleischer RC, Harmon LJ, Hendry AP, Knope ML, Mallet J, Martin C, Parent CE, Patton AH, Pfennig KS, Rubinoff D, Schluter D, Seehausen O, Shaw KL, Stacy E, Stervander M, Stroud JT, Wagner C, Wogan GOU. Comparing Adaptive Radiations Across Space, Time, and Taxa. J Hered 2020; 111:1-20. [PMID: 31958131 PMCID: PMC7931853 DOI: 10.1093/jhered/esz064] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.
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Affiliation(s)
- Rosemary G Gillespie
- University of California, Berkeley, Essig Museum of Entomology & Department of Environmental Science, Policy, and Management, Berkeley, CA
| | - Gordon M Bennett
- University of California Merced, Life and Environmental Sciences Unit, Merced, CA
| | - Luc De Meester
- University of Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belguim
| | - Jeffrey L Feder
- University of Notre Dame, Dept. of Biological Sciences, Notre Dame, IN
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
| | - Luke J Harmon
- University of Idaho, Dept. of Biological Sciences, Moscow, ID
| | | | | | | | - Christopher Martin
- University of California Berkeley, Integrative Biology and Museum of Vertebrate Zoology, Berkeley, CA
| | | | - Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA
| | - Karin S Pfennig
- University of North Carolina at Chapel Hill, Department of Biology, Chapel Hill, NC
| | - Daniel Rubinoff
- University of Hawaiʻi at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu, HI
| | | | - Ole Seehausen
- Institute of Ecology & Evolution, University of Bern, Bern, BE, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Eawag, Kastanienbaum, LU, Switzerland
| | - Kerry L Shaw
- Cornell University, Neurobiology and Behavior, Tower Road,, Ithaca, NY
| | - Elizabeth Stacy
- University of Nevada Las Vegas, School of Life Sciences, Las Vegas, NV
| | - Martin Stervander
- University of Oregon, Institute of Ecology and Evolution, Eugene, OR
| | - James T Stroud
- Washington University in Saint Louis, Biology, Saint Louis, MO
| | | | - Guinevere O U Wogan
- University of California Berkeley, Environmental Science Policy, and Management, Berkeley, CA
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Ekar JM, Price DK, Johnson MA, Stacy EA. Varieties of the highly dispersible and hypervariable tree, Metrosideros polymorpha, differ in response to mechanical stress and light across a sharp ecotone. AMERICAN JOURNAL OF BOTANY 2019; 106:1106-1115. [PMID: 31330066 DOI: 10.1002/ajb2.1331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/28/2019] [Indexed: 05/26/2023]
Abstract
PREMISE The drivers of isolation between sympatric populations of long-lived and highly dispersible conspecific plants are not well understood. In the Hawaiian Islands, the landscape-dominant tree, Metrosideros polymorpha, displays extraordinary phenotypic differences among sympatric varieties despite high dispersibility of its pollen and seeds, thereby presenting a unique opportunity to investigate how disruptive selection alone can maintain incipient forms. Stenophyllous M. polymorpha var. newellii is a recently evolved tree endemic to the waterways of eastern Hawai'i Island that shows striking neutral genetic differentiation from its ancestor, wet-forest M. polymorpha var. glaberrima, despite sympatry of these forms. We looked for evidence for, and drivers of, differential local adaptation of these varieties across the range of M. polymorpha var. newellii. METHODS For paired populations of these varieties, we compared seedling performance under contrasting light conditions and a strong water current characteristic of the riparian zone. We also conducted a reciprocal transplant experiment and contrasted adult leaf anatomy. RESULTS Results suggest that the riparian zone is harsh and that selection involving the mechanical stress of rushing water, and secondarily, light, led to significant reciprocal immigrant inviability in adjacent forest and riparian environments. The strongest adaptive divergence between varieties was seen in leaves and seedlings from the site with the sharpest ecotone, coincident with the strongest genetic isolation of M. polymorpha var. newellii observed previously. CONCLUSIONS These findings suggest that disruptive selection across a sharp ecotone contributes to the maintenance of an incipient riparian ecotype from within a continuous population of a long-lived and highly dispersible tree species.
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Affiliation(s)
- Jill M Ekar
- The Microbial and Plant Genomics Institute, University of Minnesota-Twin Cities, 1500 Gortner Avenue, Saint Paul, Minnesota, 55108, USA
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, Hawai'i, 96720, USA
| | - Donald K Price
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, Hawai'i, 96720, USA
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, Nevada, 89154, USA
| | - Melissa A Johnson
- USDA-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawai'i, 96720, USA
| | - Elizabeth A Stacy
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, Hawai'i, 96720, USA
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, Nevada, 89154, USA
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