1
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Harenčár J, Vargas OM, Escalona M, Schemske DW, Kay KM. Genome assemblies and comparison of two Neotropical spiral gingers: Costus pulverulentus and C. lasius. J Hered 2023; 114:286-293. [PMID: 36928286 PMCID: PMC10212132 DOI: 10.1093/jhered/esad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The spiral gingers (Costus L.) are a pantropical genus of herbaceous perennial monocots; the Neotropical clade of Costus radiated rapidly in the past few million years into over 60 species. The Neotropical spiral gingers have a rich history of evolutionary and ecological research that can motivate and inform modern genetic investigations. Here, we present the first 2 chromosome-level genome assemblies in the genus, for C. pulverulentus and C. lasius, and briefly compare their synteny. We assembled the C. pulverulentus genome from a combination of short-read data, Chicago and Dovetail Hi-C chromatin-proximity sequencing, and alignment with a linkage map. We annotated the genome by mapping a C. pulverulentus transcriptome and querying mapped transcripts against a protein database. We assembled the C. lasius genome with Pacific Biosciences HiFi long reads and alignment to the C. pulverulentus genome. These 2 assemblies are the first published genomes for non-cultivated tropical plants. These genomes solidify the spiral gingers as a model system and will facilitate research on the poorly understood genetic basis of tropical plant diversification.
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Affiliation(s)
- Julia Harenčár
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Oscar M Vargas
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Douglas W Schemske
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Kathleen M Kay
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States
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2
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Maas PJM, Maas-van de Kamer H, André T, Skinner D, Valderrama E, Specht CD. Eighteen new species of Neotropical Costaceae (Zingiberales). PHYTOKEYS 2023; 222:75-127. [PMID: 37252638 PMCID: PMC10210046 DOI: 10.3897/phytokeys.222.87779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/19/2023] [Indexed: 05/31/2023]
Abstract
In preparation for a full taxonomic revision of the Neotropical genera of Costaceae (i.e., Chamaecostus, Costus, Dimerocostus, and Monocostus), we present the description of 17 new species of Neotropical Costus and one new species of the Neotropic endemic genus Chamaecostus with notes on their distribution and ecology, vernacular names (when known), and diagnostic characters for identification. Distribution maps are included for all species, and each description is accompanied by photographic plates illustrating diagnostic characters.
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Affiliation(s)
- Paul J. M. Maas
- Naturalis Biodiversity Centre, Botany, P.O. Box 9517, 2300 RA Leiden, NetherlandsNaturalis Biodiversity CentreLeidenNetherlands
| | - Hiltje Maas-van de Kamer
- Naturalis Biodiversity Centre, Botany, P.O. Box 9517, 2300 RA Leiden, NetherlandsNaturalis Biodiversity CentreLeidenNetherlands
| | - Thiago André
- Universidade de Brasília, Departamento de Botânica, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília (DF), BrazilUniversidade de BrasíliaBrasíliaBrazil
| | - David Skinner
- Le Jardin Ombragé, Tallahassee, (Private botanical garden, Botanic Gardens Conservation International – BGCI – registration ID 50148), Florida, USALe Jardin OmbragéTallahasseeUnited States of America
| | - Eugenio Valderrama
- Cornell University, Section of Plant Biology and the L.H.Bailey Hortorium, School of Integrative Plant Science, Ithaca, NY, USACornell UniversityIthacaUnited States of America
| | - Chelsea D. Specht
- Cornell University, Section of Plant Biology and the L.H.Bailey Hortorium, School of Integrative Plant Science, Ithaca, NY, USACornell UniversityIthacaUnited States of America
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3
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Kay KM, Grossenbacher DL. Evolutionary convergence on hummingbird pollination in Neotropical Costus provides insight into the causes of pollinator shifts. THE NEW PHYTOLOGIST 2022; 236:1572-1583. [PMID: 36068995 PMCID: PMC9826479 DOI: 10.1111/nph.18464] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The evolution of hummingbird pollination is common across angiosperms throughout the Americas, presenting an opportunity to examine convergence in both traits and environments to better understand how complex phenotypes arise. Here we examine independent shifts from bee to hummingbird pollination in the Neotropical spiral gingers (Costus) and address common explanations for the prevalence of transitions from bee to hummingbird pollination. We use floral traits of species with observed pollinators to predict pollinators of unobserved species and reconstruct ancestral pollination states on a well-resolved phylogeny. We examine whether independent transitions evolve towards the same phenotypic optimum and whether shifts to hummingbird pollination correlate with elevation or climate. Traits predicting hummingbird pollination include small flower size, brightly colored floral bracts and the absence of nectar guides. We find many shifts to hummingbird pollination and no reversals, a single shared phenotypic optimum across hummingbird flowers, and no association between pollination and elevation or climate. Evolutionary shifts to hummingbird pollination in Costus are highly convergent and directional, involve a surprising set of traits when compared with other plants with analogous transitions and refute the generality of several common explanations for the prevalence of transitions from bee to hummingbird pollination.
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Affiliation(s)
- Kathleen M. Kay
- Department of Ecology and Evolutionary BiologyUniversity of California, Santa CruzSanta CruzCA95060USA
| | - Dena L. Grossenbacher
- Department of BiologyCalifornia Polytechnic State UniversitySan Luis ObispoCA93401USA
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4
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Dellinger AS, Paun O, Baar J, Temsch EM, Fernández-Fernández D, Schönenberger J. Population structure in Neotropical plants: integrating pollination biology, topography and climatic niches. Mol Ecol 2022; 31:2264-2280. [PMID: 35175652 PMCID: PMC9310734 DOI: 10.1111/mec.16403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/29/2022]
Abstract
Animal pollinators mediate gene flow among plant populations, but in contrast to well‐studied topographic and (Pleistocene) environmental isolating barriers, their impact on population genetic differentiation remains largely unexplored. Comparing how these multifarious factors drive microevolutionary histories is, however, crucial for better resolving macroevolutionary patterns of plant diversification. Here we combined genomic analyses with landscape genetics and niche modelling across six related Neotropical plant species (424 individuals across 33 localities) differing in pollination strategy to test the hypothesis that highly mobile (vertebrate) pollinators more effectively link isolated localities than less mobile (bee) pollinators. We found consistently higher genetic differentiation (FST) among localities of bee‐ than vertebrate‐pollinated species with increasing geographical distance, topographic barriers and historical climatic instability. High admixture among montane populations further suggested relative climatic stability of Neotropical montane forests during the Pleistocene. Overall, our results indicate that pollinators may differentially impact the potential for allopatric speciation, thereby critically influencing diversification histories at macroevolutionary scales.
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Affiliation(s)
- Agnes S Dellinger
- Department of Botany and Biodiversity Research, University of Vienna, Austria.,Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Austria
| | - Juliane Baar
- Department of Botany and Biodiversity Research, University of Vienna, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Austria
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Austria
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5
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Kay KM, Surget-Groba Y. The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understorey herbs. Mol Ecol 2021; 31:4351-4363. [PMID: 34487383 DOI: 10.1111/mec.16165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many co-adapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.
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Affiliation(s)
- Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yann Surget-Groba
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Département de Biologie, Université du Québec en Outaouais, Ripon, QC, Canada
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6
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Moreira-Hernández JI, Muchhala N. Importance of Pollinator-Mediated Interspecific Pollen Transfer for Angiosperm Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024804] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding how pollen moves between species is critical to understanding speciation, diversification, and evolution of flowering plants. For co-flowering species that share pollinators, competition through interspecific pollen transfer (IPT) can profoundly impact floral evolution, decreasing female fitness via heterospecific pollen deposition on stigmas and male fitness via pollen misplacement during visits to heterospecific flowers. The pollination literature demonstrates that such reproductive interference frequently selects for reproductive character displacement in floral traits linked to pollinator attraction, pollen placement, and mating systems and has also revealed that IPT between given pairs of species is typically asymmetric. More recent work is starting to elucidate its importance to the speciation process, clarifying the link between IPT and current and historical patterns of hybridization, the evolution of phenotypic novelty through adaptive introgression, and the rise of reproductive isolation. Our review aims to stimulate further research on IPT as a ubiquitous mechanism that plays a central role in angiosperm diversification.
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Affiliation(s)
- Juan Isaac Moreira-Hernández
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, Missouri 63121, USA;,
| | - Nathan Muchhala
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, Missouri 63121, USA;,
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7
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Zhang N, Ma Y, Folk RA, Yu J, Pan Y, Gong X. Maintenance of species boundaries in three sympatric Ligularia (Senecioneae, Asteraceae) species. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:986-999. [PMID: 29877612 DOI: 10.1111/jipb.12674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
The key process in speciation concerns the formation and maintenance of reproductive isolating barriers between diverging lineages. Although species boundaries are frequently investigated between two species across many taxa, reproductive isolating barriers among multiple species (>2) that would represent the most common phenomenon in nature, remain to be clarified. Here, we use double digest restriction-site associated DNA (ddRAD) sequencing to examine patterns of hybridization at a sympatric site where three Ligularia species grow together and verify whether those patterns contribute to the maintenance of boundaries among species. The results based on the RAD SNP datasets indicated hybridization Ligularia cyathiceps × L. duciformis and L. duciformis × L. yunnanensis were both restricted to F1 s plus a few first-generation backcrosses and no gene introgression were identified, giving rise to strong reproductive isolation among hybridizing species. Moreover, hybrid swarm simulation, using HYBRIDLAB, indicated the RAD SNP datasets had sufficient discriminatory power for accurate hybrid detection. We conclude that parental species show strong reproductive isolation and they still maintain species boundaries, which may be the key mechanism to maintain species diversity of Ligularia in the eastern Qinghai-Tibetan Plateau and adjacent areas. Moreover, this study highlights the effectiveness of RAD sequencing in hybridization studies.
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Affiliation(s)
- Ningning Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongpeng Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
| | - Ryan A Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jiaojun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
| | - Yuezhi Pan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
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8
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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9
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Opedal ØH, Falahati-Anbaran M, Albertsen E, Armbruster WS, Pérez-Barrales R, Stenøien HK, Pélabon C. Euglossine bees mediate only limited long-distance gene flow in a tropical vine. THE NEW PHYTOLOGIST 2017; 213:1898-1908. [PMID: 27997039 DOI: 10.1111/nph.14380] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Abstract
Euglossine bees (Apidae: Euglossini) have long been hypothesized to act as long-distance pollinators of many low-density tropical plants. We tested this hypothesis by the analysis of gene flow and genetic structure within and among populations of the euglossine bee-pollinated vine Dalechampia scandens. Using microsatellite markers, we assessed historical gene flow by the quantification of regional-scale genetic structure and isolation by distance among 18 populations, and contemporary gene flow by the estimation of recent migration rates among populations. To assess bee-mediated pollen dispersal on a smaller scale, we conducted paternity analyses within a focal population, and quantified within-population spatial genetic structure in four populations. Gene flow was limited to certain nearby populations within continuous forest blocks, whereas drift appeared to dominate on larger scales. Limited long-distance gene flow was supported by within-population patterns; gene flow was biased towards nearby plants, and significant small-scale spatial genetic structure was detected within populations. These findings suggest that, although female euglossine bees might be effective at moving pollen within populations, and perhaps within forest blocks, their contribution to gene flow on the regional scale seems too limited to counteract genetic drift in patchily distributed tropical plants. Among-population gene flow might have been reduced following habitat fragmentation.
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Affiliation(s)
- Øystein H Opedal
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Mohsen Falahati-Anbaran
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, University of Tehran, 14155-6455, Tehran, Iran
| | - Elena Albertsen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - W Scott Armbruster
- Department of Biology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Rocío Pérez-Barrales
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK
| | - Hans K Stenøien
- Department of Natural History, NTNU University Museum, 7491, Trondheim, Norway
| | - Christophe Pélabon
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
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10
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Fu PC, Gao QB, Zhang FQ, Xing R, Wang JL, Liu HR, Chen SL. Gene Flow Results in High Genetic Similarity between Sibiraea (Rosaceae) Species in the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2016; 7:1596. [PMID: 27826314 PMCID: PMC5078775 DOI: 10.3389/fpls.2016.01596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP) was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of Sibiraea laevigata and Sibiraea angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45%) rather than between species (4.39%). We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of the 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of the complex resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures occurred. This study sheds light on speciation with gene flow in the QTP.
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Affiliation(s)
- Peng-Cheng Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- College of Life Science, Luoyang Normal UniversityLuoyang, China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Jiu-Li Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Hai-Rui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
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11
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André T, Salzman S, Wendt T, Specht CD. Speciation dynamics and biogeography of Neotropical spiral gingers (Costaceae). Mol Phylogenet Evol 2016; 103:55-63. [PMID: 27400627 DOI: 10.1016/j.ympev.2016.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
Species can arise via the divisive effects of allopatry as well as due to ecological and/or reproductive character displacement within sympatric populations. Two separate lineages of Costaceae are native to the Neotropics; an early-diverging clade endemic to South America (consisting of ca. 16 species in the genera Monocostus, Dimerocostus and Chamaecostus); and the Neotropical Costus clade (ca. 50 species), a diverse assemblage of understory herbs comprising nearly half of total familial species richness. We use a robust dated molecular phylogeny containing most of currently known species to inform macroevolutionary reconstructions, enabling us to examine the context of speciation in Neotropical lineages. Analyses of speciation rate revealed a significant variation among clades, with a rate shift at the most recent common ancestor of the Neotropical Costus clade. There is an overall predominance of allopatric speciation in the South American clade, as most species display little range overlap. In contrast, sympatry is much higher within the Neotropical Costus clade, independent of node age. Our results show that speciation dynamics during the history of Costaceae is strongly heterogeneous, and we suggest that the Costus radiation in the Neotropics arose at varied geographic contexts.
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Affiliation(s)
- Thiago André
- Departments of Plant and Microbial Biology and Integrative Biology, University of California at Berkeley, 431 Koshland Hall, Berkeley, CA 94720-3102, USA.
| | - Shayla Salzman
- Departments of Plant and Microbial Biology and Integrative Biology, University of California at Berkeley, 431 Koshland Hall, Berkeley, CA 94720-3102, USA.
| | - Tânia Wendt
- Departamento de Botânica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Sala A1-050, Bloco A, CCS, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Chelsea D Specht
- Departments of Plant and Microbial Biology and Integrative Biology, University of California at Berkeley, 431 Koshland Hall, Berkeley, CA 94720-3102, USA.
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12
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Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests. PLoS One 2016; 11:e0156913. [PMID: 27305092 PMCID: PMC4909291 DOI: 10.1371/journal.pone.0156913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/20/2016] [Indexed: 01/24/2023] Open
Abstract
Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species’ gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees’ lifetimes.
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Twyford AD, Kidner CA, Ennos RA. Maintenance of species boundaries in a Neotropical radiation of Begonia. Mol Ecol 2016; 24:4982-93. [PMID: 26301313 PMCID: PMC4600226 DOI: 10.1111/mec.13355] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 01/04/2023]
Abstract
A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by-product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later-generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.
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Affiliation(s)
- Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.,Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.,Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.,Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Richard A Ennos
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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Turchetto C, Fagundes NJR, Segatto ALA, Kuhlemeier C, Solís Neffa VG, Speranza PR, Bonatto SL, Freitas LB. Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae). Mol Ecol 2015; 23:374-89. [PMID: 24372681 DOI: 10.1111/mec.12632] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 11/30/2022]
Abstract
Understanding the spatiotemporal distribution of genetic variation and the ways in which this distribution is connected to the ecological context of natural populations is fundamental for understanding the nature and mode of intraspecific and, ultimately, interspecific differentiation. The Petunia axillaris complex is endemic to the grasslands of southern South America and includes three subspecies: P. a. axillaris, P. a. parodii and P. a. subandina. These subspecies are traditionally delimited based on both geography and floral morphology, although the latter is highly variable. Here, we determined the patterns of genetic (nuclear and cpDNA), morphological and ecological (bioclimatic) variation of a large number of P. axillaris populations and found that they are mostly coincident with subspecies delimitation. The nuclear data suggest that the subspecies are likely independent evolutionary units, and their morphological differences may be associated with local adaptations to diverse climatic and/or edaphic conditions and population isolation. The demographic dynamics over time estimated by skyline plot analyses showed different patterns for each subspecies in the last 100 000 years, which is compatible with a divergence time between 35 000 and 107 000 years ago between P. a. axillaris and P. a. parodii, as estimated with the IMa program. Coalescent simulation tests using Approximate Bayesian Computation do not support previous suggestions of extensive gene flow between P. a. axillaris and P. a. parodii in their contact zone.
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Affiliation(s)
- Caroline Turchetto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Ana L A Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, Altenbergrain 21 CH-3013, Bern, Switzerland
| | - Viviana G Solís Neffa
- Instituto de Botánica del Nordeste (UNNE-CONICET), Sargento Cabral 2131, Corrientes, 3400, Argentina
| | - Pablo R Speranza
- Facultad de Agronomía, Universidad de la República, Av. E. Garzón 780, Montevideo, 12900, Uruguay
| | - Sandro L Bonatto
- Laboratory of Genomic and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul, Ipiranga 6681, Porto Alegre, RS, 90610-001, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, 91501-970, Porto Alegre, RS, Brazil
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15
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Pellissier L. Stability and the competition-dispersal trade-off as drivers of speciation and biodiversity gradients. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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16
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Strong postzygotic isolation prevents introgression between two hybridizing Neotropical orchids, Epidendrum denticulatum and E. fulgens. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9753-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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