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Levin RA, Miller JS. Molecular signatures of long-distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum. AMERICAN JOURNAL OF BOTANY 2021; 108:694-710. [PMID: 33811320 DOI: 10.1002/ajb2.1626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Long-distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of Lycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems. METHODS We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome-wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the S-RNase mating system gene. RESULTS Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and the S-RNase locus due to a colonization bottleneck and the loss of self-incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self-incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico. CONCLUSIONS Long-distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of L. carolinianum. The collapse of diversity at the S-RNase locus in island populations suggests that self-fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.
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Affiliation(s)
- Rachel A Levin
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
| | - Jill S Miller
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
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Garot E, Joët T, Combes MC, Lashermes P. Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors. Heredity (Edinb) 2019; 122:833-847. [PMID: 30478354 PMCID: PMC6781115 DOI: 10.1038/s41437-018-0168-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/09/2018] [Indexed: 01/23/2023] Open
Abstract
Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.
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Affiliation(s)
- Edith Garot
- IRD, University of Montpellier, DIADE, Montpellier, France
| | - Thierry Joët
- IRD, University of Montpellier, DIADE, Montpellier, France
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Abstract
The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-by-step demonstration of how to build a simple evolutionary model in SLiM 3, to help new users get started. We will begin with a panmictic neutral model, and build up to a model of the evolution of a polygenic quantitative trait under selection for an environmental phenotypic optimum.
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Affiliation(s)
- Benjamin C Haller
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY
| | - Philipp W Messer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY
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Miller JS, Blank CM, Levin RA. Colonization, Baker's law, and the evolution of gynodioecy in Hawaii: implications from a study of Lycium carolinianum. AMERICAN JOURNAL OF BOTANY 2019; 106:733-743. [PMID: 31042317 DOI: 10.1002/ajb2.1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
PREMISE As Baker's law suggests, the successful colonization of oceanic islands is often associated with uniparental reproduction (self-fertility), but the high incidence of dimorphism (dioecy, gynodioecy) on islands complicates this idea. Lycium carolinianum is widespread, occurring on the North American mainland and the Hawaiian Islands. We examined Baker's ideas for mainland and island populations of L. carolinianum and examined inbreeding depression as a possible contributor to the evolution of gynodioecy on Maui. METHODS Controlled crosses were conducted in two mainland populations and two populations in Hawaii. Treatments included self and cross pollination, unmanipulated controls, and autogamy/agamospermy. Alleles from the self-incompatibility S-RNase gene were isolated and compared between mainland and island populations. Given self-compatibility in Hawaii, we germinated seeds from self- and cross- treatments and estimated inbreeding depression using seven traits and a measure of cumulative fitness. RESULTS Mainland populations of Lycium carolinianum are predominately self-incompatible with some polymorphism for self-fertility, whereas Hawaiian populations are self-compatible. Concordantly, S-RNase allelic diversity is reduced in Hawaii compared to the mainland. Hawaiian populations also exhibit significant inbreeding depression. CONCLUSIONS Self-compatibility in Hawaii and individual variation in self-fertility in mainland populations suggests that a colonization filter promoting uniparental reproduction may be acting in this system. Comparison of S-RNase variation suggests a collapse of allelic diversity and heterozygosity at the S-RNase locus in Hawaii, which likely contributed to mate limitation upon arrival to the Pacific. Inbreeding depression coupled with autonomous self-fertilization may have led to the evolution of gynodioecy on Maui.
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Affiliation(s)
- Jill S Miller
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
| | - Caitlin M Blank
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Rachel A Levin
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
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Haller BC, Galloway J, Kelleher J, Messer PW, Ralph PL. Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Mol Ecol Resour 2019; 19:552-566. [PMID: 30565882 PMCID: PMC6393187 DOI: 10.1111/1755-0998.12968] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/12/2022]
Abstract
There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using "recapitation"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.
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Affiliation(s)
- Benjamin C. Haller
- Dept. of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jared Galloway
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7FZ, UK
| | - Philipp W. Messer
- Dept. of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Peter L. Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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Grossenbacher DL, Brandvain Y, Auld JR, Burd M, Cheptou PO, Conner JK, Grant AG, Hovick SM, Pannell JR, Pauw A, Petanidou T, Randle AM, Rubio de Casas R, Vamosi J, Winn A, Igic B, Busch JW, Kalisz S, Goldberg EE. Self-compatibility is over-represented on islands. THE NEW PHYTOLOGIST 2017; 215:469-478. [PMID: 28382619 DOI: 10.1111/nph.14534] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/20/2017] [Indexed: 06/07/2023]
Abstract
Because establishing a new population often depends critically on finding mates, individuals capable of uniparental reproduction may have a colonization advantage. Accordingly, there should be an over-representation of colonizing species in which individuals can reproduce without a mate, particularly in isolated locales such as oceanic islands. Despite the intuitive appeal of this colonization filter hypothesis (known as Baker's law), more than six decades of analyses have yielded mixed findings. We assembled a dataset of island and mainland plant breeding systems, focusing on the presence or absence of self-incompatibility. Because this trait enforces outcrossing and is unlikely to re-evolve on short timescales if it is lost, breeding system is especially likely to reflect the colonization filter. We found significantly more self-compatible species on islands than mainlands across a sample of > 1500 species from three widely distributed flowering plant families (Asteraceae, Brassicaceae and Solanaceae). Overall, 66% of island species were self-compatible, compared with 41% of mainland species. Our results demonstrate that the presence or absence of self-incompatibility has strong explanatory power for plant geographical patterns. Island floras around the world thus reflect the role of a key reproductive trait in filtering potential colonizing species in these three plant families.
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Affiliation(s)
- Dena L Grossenbacher
- Department of Biology, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Josh R Auld
- Department of Biology, West Chester University, West Chester, PA, 19383, USA
| | - Martin Burd
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Pierre-Olivier Cheptou
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valery Montpellier, EPHE, CEFE, 34293, Montpellier Cedex 05, France
| | - Jeffrey K Conner
- Kellogg Biological Station and Department of Plant Biology, Michigan State University, Hickory Corners, MI, 49060, USA
| | - Alannie G Grant
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Stephen M Hovick
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Anton Pauw
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Theodora Petanidou
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, 81100, Mytilene, Lesvos, Greece
| | - April M Randle
- Department of Environmental Science, University of San Francisco, San Francisco, CA, 94117, USA
| | - Rafael Rubio de Casas
- Departmento Ecología, Facultad de Ciencias, Universidad de Granada, Granada, UGR, 18071, Granada, Spain
| | - Jana Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada, T2N 1N4
| | - Alice Winn
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Boris Igic
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Susan Kalisz
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 2017; 109:351-361. [PMID: 28212875 DOI: 10.1016/j.ympev.2017.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
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Affiliation(s)
- Perla Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.
| | | | | | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Hosahalli L Sreenath
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India.
| | - Piet Stoffelen
- Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium.
| | - Sharon E Mitchell
- Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA.
| | | | - Serge Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | | | | | - Michel Rigoreau
- Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France.
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia.
| | | | - Romain Guyot
- UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
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Berger BA, Kriebel R, Spalink D, Sytsma KJ. Divergence times, historical biogeography, and shifts in speciation rates of Myrtales. Mol Phylogenet Evol 2015; 95:116-36. [PMID: 26585030 DOI: 10.1016/j.ympev.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 10/04/2015] [Indexed: 01/22/2023]
Abstract
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.
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Affiliation(s)
- Brent A Berger
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11432, USA; Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Daniel Spalink
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
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