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Lakušić D, Zbiljić M, Šatović Z, Kuzmanović N, Liber Z. Asymmetric Introgression and Cryptic Natural Hybridization between Two Species of Teucrium Section Polium (Lamiaceae) on the Balkan Peninsula. PLANTS (BASEL, SWITZERLAND) 2024; 13:1617. [PMID: 38931049 PMCID: PMC11207346 DOI: 10.3390/plants13121617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
In this work, we analyzed the morphology and genetic structure of Teucrium montanum, T. capitatum and their hybrid T. × rohlenae from three syntopic populations. A morphometric study showed that the parents and their hybrids exhibited continuous morphological variation, with the hybrid positioned exactly between the parents. Genetic analysis revealed that plants morphologically identified as T. × rohlenae are fertile hybrids that produce hybrid swarms dominated by later-generation hybrids. This suggests that introgression, rather than speciation, is the more likely outcome of hybridization between these plant species. The extent and direction of gene flow between the two species differed markedly between the three syntopic localities. At the Trilj locality, it was clearly unidirectional, with T. capitatum playing the dominant role. At the Sićevo locality, gene flow was slightly asymmetric, favoring the genetic background of T. capitatum, while at the Sliven site, it was completely asymmetric in the opposite direction. The extreme case of unidirectional gene flow was observed at the Trilj locality where plants morphologically identified as T. montanum could not be genetically distinguished from T. capitatum. This suggests that interspecific hybridization occurred long ago, leading to introgression and cryptic hybrids, blurring of species boundaries and generating evolutionary noise.
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Affiliation(s)
- Dmitar Lakušić
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Takovska 43, 11000 Belgrade, Serbia; (D.L.); (N.K.)
| | - Miloš Zbiljić
- Department of Botany, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11060 Belgrade, Serbia;
| | - Zlatko Šatović
- Department of Plant Biodiversity, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia;
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska 25, 10000 Zagreb, Croatia
| | - Nevena Kuzmanović
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Takovska 43, 11000 Belgrade, Serbia; (D.L.); (N.K.)
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska 25, 10000 Zagreb, Croatia
- Division of Botany, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9A, 10000 Zagreb, Croatia
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Belokon MM, Belokon YS, Petrova EA, Vasilyeva GV, Efimova AP, Zakharov ES, Goroshkevich SN, Politov DV. Ancient and Modern Hybridization of Siberian Stone Pine and Dwarf Siberian Pine in the South of Yakutia. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422110023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Genome-wide analyses of introgression between two sympatric Asian oak species. Nat Ecol Evol 2022; 6:924-935. [PMID: 35513577 DOI: 10.1038/s41559-022-01754-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In particular, we are yet to determine the genomic distribution of introgressed regions along the genome; whether the extent and patterns of introgression are influenced by ecological factors; and when and how introgression contributes to adaptation. Here, we generated high-quality genomic resources for two sympatric widespread Asian oak species, Quercus acutissima and Q. variabilis, sampled in multiple forests to study introgression between them. We show that introgressed regions are broadly distributed across the genome. Introgression was affected by genetic divergence between pairs of populations and by the similarity of the environments in which they live-populations occupying similar ecological sites tended to share the same introgressed regions. Introgressed genomic footprints of adaptation were preferentially located in regions with suppressed recombination rate. Introgression probably confers adaptation in these oak populations by introducing allelic variation in cis-regulatory elements, in particular through transposable element insertions, thereby altering the regulation of genes related to stress. Our results provide new avenues of research for uncovering mechanisms of adaptation due to hybridization in sympatric species.
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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5
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Kikuchi S, Osone Y. Subspecies divergence and pronounced phylogenetic incongruence in the East-Asia-endemic shrub Magnolia sieboldii. ANNALS OF BOTANY 2021; 127:75-90. [PMID: 32966556 PMCID: PMC7750721 DOI: 10.1093/aob/mcaa174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS The biogeographic patterns of the East-Asia-endemic shrub Magnolia sieboldii, in which the range of the subsp. sieboldii is interposed with the disjunct distribution of subsp. japonica, implies a complex evolutionary history, involving rapid speciation and hybridization. Here, we aim to reveal the evolutionary and phylogeographic histories of the species with a particular focus on the time of subspecies divergence, the hypothesis of secondary hybridization and the Pleistocene survival of each subspecies, using a combination of genetic analyses and ecological niche modelling. METHODS Genetic variation, genetic structures and phylogenetic relationships were elucidated based on nuclear low-copy genes, chloroplast DNA, and nuclear simple sequence repeats (SSRs). A scenario selection analysis and divergence time estimation were performed using coalescent simulation in DIYABC and *BEAST. Ecological niche modelling and a test of niche differentiation were performed using Maxent and ENMTools. KEY RESULTS All marker types showed deep, but pronouncedly incongruent, west-east genetic divergences, with the subspecies being delineated only by the nuclear low-copy genes. Phylogenetic tree topologies suggested that ancient hybridization and introgression were likely to have occurred; however, this scenario did not receive significant support in the DIYABC analysis. The subspecies differentiated their niches, but both showed a dependence on high humidity and were predicted to have persisted during the last glacial cycle by maintaining a stable latitudinal distribution via migration to lower altitudes. CONCLUSIONS We found a deep genetic divergence and a pronounced phylogenetic incongruence among the two subspecies of M. sieboldii, which may have been driven by major paleogeographic and paleoclimatic events that have occurred since the Neogene in East Asia, including global cooling, climate oscillations and the formation of land bridges. Both subspecies were, however, considered to persist in situ in stable climatic conditions during the late Pleistocene.
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Affiliation(s)
- Satoshi Kikuchi
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba City, Ibaraki Prefecture, Japan
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitsujigaoka, Toyohira, Sapporo City, Hokkaido, Japan
| | - Yoko Osone
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba City, Ibaraki Prefecture, Japan
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Feng YY, Shen TT, Shao CC, Du H, Ran JH, Wang XQ. Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution. Mol Phylogenet Evol 2020; 157:107066. [PMID: 33387645 DOI: 10.1016/j.ympev.2020.107066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/26/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022]
Abstract
The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Cheng-Cheng Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Farhat P, Siljak-Yakovlev S, Valentin N, Fabregat C, Lopez-Udias S, Salazar-Mendias C, Altarejos J, Adams RP. Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations. BMC Evol Biol 2020; 20:148. [PMID: 33167862 PMCID: PMC7650182 DOI: 10.1186/s12862-020-01688-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main areas were studied in Spain (Eastern Iberian Range and Sierra de Baza) with both diploid and tetraploid taxa present in sympatry. Gene flow and ploidy level were assessed for these taxa and the resulted offspring. RESULTS Twenty-two allo-triploid hybrids between J. sabina var. sabina and J. thurifera were found in the Eastern Iberian Range population. However, in the Sierra de Baza population no triploids were found. Instead, 18 allo-tetraploid hybrids between two tetraploid taxa: J. sabina var. balkanensis and J. thurifera were discovered. High genetic diversity was exhibited among the tetraploid hybrids at Sierra de Baza, in contrast to the genetically identical triploid hybrids at the Eastern Iberian Range; this suggests meiotic difficulties within the triploid hybrids. In addition, unidirectional gene flow was observed in both studied areas. CONCLUSION Polyploidy and hybridization can be complementary partners in the evolution of Juniperus taxa in sympatric occurrences. Juniperus was shown to be an ideal coniferous model to study these two phenomena, independently or in concert.
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Affiliation(s)
- Perla Farhat
- Biology Department, Baylor University, Waco, TX, 76798, USA.
- Present address: Key Laboratory of Bio-resources and Eco-environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91405, Orsay, France
| | - Nicolas Valentin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Carlos Fabregat
- Jardí Botànic de la Universitat de València, 46008, València, Spain
| | | | - Carlos Salazar-Mendias
- Departamento de Biología Animal, Biología Vegetal y Ecología. Universidad de Jaén, 23071, Jaén, Spain
| | - Joaquín Altarejos
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071, Jaén, Spain
| | - Robert P Adams
- Biology Department, Baylor University, Waco, TX, 76798, USA
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Godbout J, Gros-Louis M, Lamothe M, Isabel N. Going with the flow: Intraspecific variation may act as a natural ally to counterbalance the impacts of global change for the riparian species Populus deltoides. Evol Appl 2020; 13:176-194. [PMID: 31892951 PMCID: PMC6935597 DOI: 10.1111/eva.12854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/16/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022] Open
Abstract
The speed and magnitude of global change will have major impacts on riparian ecosystems, thereby leading to greater forest vulnerability. Assessing species' adaptive capacities to provide relevant information for vulnerability assessments remains challenging, especially for nonmodel species like the North American Populus deltoides W. Bartram ex Marshall. The objective of this study was to understand how genomic diversity of this foundation species was shaped by its environment (climate, soil, and biotic interactions) to gauge its adaptive capacity. We used two complementary approaches to get a full portrait of P. deltoides genetic diversity at both the species and whole-genome ranges. First, we used a set of 93 nuclear and three chloroplastic SNP markers in 946 individuals covering most of the species' natural distribution. Then, to measure the degree of intraspecific divergence at the whole-genome level and to support the outlier and genomic-environment association analyses, we used a sequence capture approach on DNA pools. Three distinct lineages for P. deltoides were detected, and their current distribution was associated with abiotic and biotic variations. The comparison between both cpDNA and ncDNA patterns showed that gene flow between the lineages is unbalanced. The southern and northeastern populations may benefit from the input, through river flow, of novel alleles located upstream to their local gene pools. These alleles could migrate from populations that are already adapted to conditions that fit the predicted climates in the receiving local populations, hotter at the northeastern limit and drier in the Central United States. These "preadapted" incoming alleles may help to cope with maladaptation in populations facing changing conditions.
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Affiliation(s)
- Julie Godbout
- Ministère des Forêts, de la Faune et des Parcs, Direction de la recherche forestièreQuébecQCCanada
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaQuébecQCCanada
| | | | - Manuel Lamothe
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaQuébecQCCanada
| | - Nathalie Isabel
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaQuébecQCCanada
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Li M, Xie D, Xie C, Deng Y, Zhong Y, Yu Y, He X. A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Alliums (Amaryllidaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:149. [PMID: 30891047 PMCID: PMC6412145 DOI: 10.3389/fpls.2019.00149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/28/2019] [Indexed: 05/20/2023]
Abstract
The Qinghai-Tibet Plateau (QTP) has been biogeographically divided into the eastern monsoonal and the western continental climatic zones along the 500 mm isohyet. However, this biogeographic hypothesis has been rarely tested using a phylogeographic approach. The members of the genus Allium subgenus Cyathophora coincidentally distribute across this biogeographical divide. Intriguingly, Allium fasciculatum of subgenus Amerallium co-occurs in the distribution range of subgenus Cyathophora. To illuminate the role of this biogeographic divide on the genetic divergence, we genotyped 466 individuals of 52 populations of subgenus Cyathophora and 110 individuals of 19 populations of A. fasciculatum using three chloroplast DNA fragments, whole nrITS and nine nuclear microsatellite loci, supplemented with the present environmental space and paleo-distribution modeling. Our phylogeographical evidence recovered the concordant east-west genetic breaks both for subgenus Cyathophora and A. fasciculatum along the 500 mm isohyet. The divergence time estimations and environmental niche differentiations suggested this east-west genetic breaks could have been triggered by the climatic-induced vicariance during the early Pleistocene. Noticeably, this split within subgenus Cyathophora could have been deepened by the morphological vicariance from the eastern umbel to the western spicate, while that within A. fasciculatum could have been obscured due to the pollen flows from the east to west caused by the postglacial expansion. The genetic structures and ecological niche modelings (ENMs) recovered the distinct responses to the Quaternary climatic oscillations for species constricted to different climatic zones, further highlighting the profound effect of the climatic differences and tectonic uplifts on the genetic diversification. Overall, our findings offer strong evidence for the existence of a biogeographic divide between the eastern monsoonal and the west continental climatic zones of the QTP nearly along the 500 mm isohyet.
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Bentz BJ, Hood SM, Hansen EM, Vandygriff JC, Mock KE. Defense traits in the long-lived Great Basin bristlecone pine and resistance to the native herbivore mountain pine beetle. THE NEW PHYTOLOGIST 2017; 213:611-624. [PMID: 27612209 PMCID: PMC5213150 DOI: 10.1111/nph.14191] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/05/2016] [Indexed: 05/11/2023]
Abstract
Mountain pine beetle (MPB, Dendroctonus ponderosae) is a significant mortality agent of Pinus, and climate-driven range expansion is occurring. Pinus defenses in recently invaded areas, including high elevations, are predicted to be lower than in areas with longer term MPB presence. MPB was recently observed in high-elevation forests of the Great Basin (GB) region, North America. Defense and susceptibility in two long-lived species, GB bristlecone pine (Pinus longaeva) and foxtail pine (P. balfouriana), are unclear, although they are sympatric with a common MPB host, limber pine (P. flexilis). We surveyed stands with sympatric GB bristlecone-limber pine and foxtail-limber pine to determine relative MPB attack susceptibility and constitutive defenses. MPB-caused mortality was extensive in limber, low in foxtail and absent in GB bristlecone pine. Defense traits, including constitutive monoterpenes, resin ducts and wood density, were higher in GB bristlecone and foxtail than in limber pine. GB bristlecone and foxtail pines have relatively high levels of constitutive defenses which make them less vulnerable to climate-driven MPB range expansion relative to other high-elevation pines. Long-term selective herbivore pressure and exaptation of traits for tree longevity are potential explanations, highlighting the complexity of predicting plant-insect interactions under climate change.
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Affiliation(s)
- Barbara J. Bentz
- USDA Forest Service Rocky Mountain Research StationLoganUT84321USA
| | - Sharon M. Hood
- USDA Forest Service Rocky Mountain Research StationMissoulaMT59808USA
| | | | | | - Karen E. Mock
- Department of Wildland Resources and Ecology CenterUtah State UniversityLoganUT84321USA
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de Lafontaine G, Prunier J, Gérardi S, Bousquet J. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana×P. rubens). Mol Ecol 2015; 24:5229-47. [DOI: 10.1111/mec.13377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 09/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
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12
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Cinget B, de Lafontaine G, Gérardi S, Bousquet J. Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs. Mol Ecol 2015; 24:2856-70. [DOI: 10.1111/mec.13194] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Benjamin Cinget
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
| | - Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
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13
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Cinget B, Gérardi S, Beaulieu J, Bousquet J. Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America. PLoS One 2015; 10:e0122815. [PMID: 25849816 PMCID: PMC4388536 DOI: 10.1371/journal.pone.0122815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/23/2015] [Indexed: 11/18/2022] Open
Abstract
The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.
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Affiliation(s)
- Benjamin Cinget
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
- Natural Resources Canada, Canadian Wood Fibre Centre, Canadian Wood Fibre Centre, Natural Resources Canada, Québec, Québec, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
- * E-mail:
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14
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van Loo M, Hintsteiner W, Pötzelsberger E, Schüler S, Hasenauer H. Intervarietal and intravarietal genetic structure in Douglas-fir: nuclear SSRs bring novel insights into past population demographic processes, phylogeography, and intervarietal hybridization. Ecol Evol 2015; 5:1802-17. [PMID: 26140197 PMCID: PMC4485962 DOI: 10.1002/ece3.1435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 10/23/2014] [Accepted: 01/21/2015] [Indexed: 01/22/2023] Open
Abstract
Douglas-fir (Pseudotsuga menziesii) is one of numerous wide-range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression. Thirty-eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9–40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice-covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management.
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Affiliation(s)
- Marcela van Loo
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
| | - Wolfgang Hintsteiner
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria ; alpS-GmbH Grabenweg 68, 6020, Innsbruck, Austria
| | - Elisabeth Pötzelsberger
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes Hauptstr. 7, 1140, Vienna, Austria
| | - Hubert Hasenauer
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
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15
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Aizawa M, Yoshimaru H, Takahashi M, Kawahara T, Sugita H, Saito H, Sabirov RN. Genetic structure of Sakhalin spruce (Picea glehnii) in northern Japan and adjacent regions revealed by nuclear microsatellites and mitochondrial gene sequences. JOURNAL OF PLANT RESEARCH 2015; 128:91-102. [PMID: 25421922 DOI: 10.1007/s10265-014-0682-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 09/09/2014] [Indexed: 06/04/2023]
Abstract
The genetic structure of Sakhalin spruce (Picea glehnii) was studied across the natural range of the species, including two small isolated populations in south Sakhalin and Hayachine, by using six microsatellite loci and maternally inherited mitochondrial gene sequences. We also analyzed P. jezoensis, a sympatric spruce in the range. Genetic diversity of P. glehnii was higher in central Hokkaido and the lowest in the Hayachine. Bayesian clustering and principal coordinate analysis by using the microsatellites indicated that the Hayachine was clearly distinct from other populations, implying that it had undergone strong genetic drift since the last glacial period. P. glehnii harbored four mitochondrial haplotypes, two of which were shared with P. jezoensis. One of the two was observed without geographical concentration, suggesting its derivation from ancestral polymorphism. Another was observed in south Sakhalin and in P. jezoensis across Sakhalin. The Bayesian clustering--by using four microsatellite loci, including P. jezoensis populations--indicated unambiguous species delimitation, but with possible admixture of P. jezoensis genes into P. glehnii in south Sakhalin, where P. glehnii is abundantly overwhelmed by P. jezoensis; this might explain the occurrence of introgression of the haplotype of P. jezoensis into P. glehnii.
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Affiliation(s)
- Mineaki Aizawa
- Department of Forest Science, Faculty of Agriculture, Utsunomiya University, 350, Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan,
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16
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Wang B, Wang XR. Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus. Mol Phylogenet Evol 2014; 80:20-30. [PMID: 25106134 DOI: 10.1016/j.ympev.2014.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/18/2014] [Accepted: 07/24/2014] [Indexed: 11/28/2022]
Abstract
The evolution of the mitochondrial (mt) genome is far from being fully understood. Systematic investigations into the modes of inheritance, rates and patterns of recombination, nucleotide substitution, and structural changes in the mt genome are still lacking in many groups of plants. In this study, we sequenced >11kbp mtDNA segments from multiple accessions of 36 pine species to characterize the evolutionary patterns of mtDNA in the genus Pinus. We found extremely low substitution rates and complex repetitive sequences scattered across different genome regions, as well as chimeric structures that were probably generated by multiple intergenomic recombinations. The mtDNA-based phylogeny of the genus differed from that based on chloroplast and nuclear DNA in the placement of several groups of species. Such discordances suggest a series of mtDNA capture events during past range shifts of the pine species and that both vertical and horizontal inheritance are implicated in the evolution of mtDNA in Pinus. MtDNA dating revealed that most extant lineages of the genus originated during Oligocene-Miocene radiation and subgenus Strobus diversified earlier than subgenus Pinus. Our findings illustrate a reticular evolutionary pathway for the mt genome through capture and recombination in the genus Pinus, and provide new insights into the evolution of the genus.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden.
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
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Rona LDP, Carvalho-Pinto CJ, Peixoto AA. Evidence for the occurrence of two sympatric sibling species within the Anopheles (Kerteszia) cruzii complex in southeast Brazil and the detection of asymmetric introgression between them using a multilocus analysis. BMC Evol Biol 2013; 13:207. [PMID: 24063651 PMCID: PMC3850420 DOI: 10.1186/1471-2148-13-207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 08/21/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Anopheles (Kerteszia) cruzii (Diptera: Culicidae) is a primary vector of human and simian malaria parasites in southern and southeastern Brazil. Earlier studies using chromosome inversions, isoenzymes and a number of molecular markers have suggested that An. cruzii is a species complex. RESULTS In this study, a multilocus approach using six loci, three circadian clock genes and three encoding ribosomal proteins, was carried out to investigate in more detail the genetic differentiation between the An. cruzii populations from Florianópolis-Santa Catarina (southern Brazil) and Itatiaia-Rio de Janeiro States (southeastern Brazil). The analyses were performed first comparing Florianópolis and Itatiaia, and then comparing the two putative sympatric incipient species from Itatiaia (Itatiaia A and Itatiaia B). The analysis revealed high FST values between Florianópolis and Itatiaia (considering Itatiaia A and B together) and also between the sympatric Itatiaia A and Itatiaia B, irrespective of their function. Also, using the IM program, no strong indication of migration was found between Florianópolis and Itatiaia (considering Itatiaia A and B together) using all loci together, but between Itatiaia A and Itatiaia B, the results show evidence of migration only in the direction of Itatiaia B. CONCLUSIONS The results of the multilocus analysis indicate that Florianópolis and Itatiaia represent different species of the An. cruzii complex that diverged around 0.6 Mya, and also that the Itatiaia sample is composed of two sympatric incipient species A and B, which diverged around 0.2 Mya. Asymmetric introgression was found between the latter two species despite strong divergence in some loci.
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Affiliation(s)
- Luísa D P Rona
- Universidade Federal do Rio de Janeiro, Polo de Xerém, Estrada de Xerém 27, Duque de Caxias 25245-390, RJ, Brazil.
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