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Yoder JB, Dang A, MacGregor C, Plaza M. Plant‐associate interactions and diversification across trophic levels. Evol Lett 2022; 6:375-389. [PMID: 36254257 PMCID: PMC9554764 DOI: 10.1002/evl3.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/27/2022] [Indexed: 11/11/2022] Open
Abstract
Interactions between species are widely understood to have promoted the diversification of life on Earth, but how interactions spur the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled population genetic studies of host plants and intimately associated herbivores, parasites, and mutualists. We used Bayesian multiple regressions and the BEDASSLE modeling framework to test whether host and associate population structures were correlated over and above the potentially confounding effects of geography and shared environmental variation. We found that associates' population structure often paralleled their hosts' population structure, and that this effect is robust to accounting for geographic distance and climate. Associate genetic structure was significantly explained by plant genetic structure somewhat more often in antagonistic interactions than in mutualistic ones. This aligns with a key prediction of coevolutionary theory that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions more often promote diversity via the effect of hosts' geographic distribution on mutualists' dispersal.
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Affiliation(s)
- Jeremy B. Yoder
- Department of Biology California State University Northridge Northridge CA 91330 USA
| | - Albert Dang
- Department of Biology California State University Northridge Northridge CA 91330 USA
| | - Caitlin MacGregor
- Department of Biology California State University Northridge Northridge CA 91330 USA
| | - Mikhail Plaza
- Program in Plant Biology and Conservation Northwestern University Evanston IL 60208 USA
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60035 USA
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2
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Teixeira‐Costa L, Heberling JM, Wilson CA, Davis CC. Parasitic flowering plant collections embody the extended specimen. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luiza Teixeira‐Costa
- Harvard University Herbaria Cambridge MA USA
- Hanse‐Wissenschaftskolleg – Institute for Advanced Study, Lehmkuhlenbusch 4, 27753 Delmenhorst Germany
| | | | - Carol A. Wilson
- University and Jepson Herbaria University of California, Berkeley, 1001 Valley Life Sciences Building Berkeley CA USA
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3
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Piwowarczyk R, Schneider AC, Góralski G, Kwolek D, Denysenko-Bennett M, Burda A, Ruraż K, Joachimiak AJ, Pedraja ÓS. Phylogeny and historical biogeography analysis support Caucasian and Mediterranean centres of origin of key holoparasitic Orobancheae (Orobanchaceae) lineages. PHYTOKEYS 2021; 174:165-194. [PMID: 33776529 PMCID: PMC7979677 DOI: 10.3897/phytokeys.174.62524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/14/2021] [Indexed: 05/28/2023]
Abstract
The extensive diversity of the tribe Orobancheae, the most species-rich lineage of holoparasitic Orobanchaceae, is concentrated in the Caucasus and Mediterranean regions of the Old World. This extant diversity has inspired hypotheses that these regions are also centres of origin of its key lineages, however the ability to test hypotheses has been limited by a lack of sampling and phylogenetic information about the species, especially in the Caucasus region. First, we assessed the phylogenetic relationships of several poorly known, problematic, or newly described species and host-races of four genera of Orobancheae occurring in the Caucasus region-Cistanche, Phelypaea, Phelipanche and Orobanche-using nuclear ribosomal (ITS) and plastid (trnL-trnF) sequence data. Then we applied a probablistic dispersal-extinction-cladogenesis model of historical biogeography across a more inclusive clade of holoparasites, to explicitly test hypotheses of Orobancheae diversification and historical biogeography shifts. In sum, we sampled 548 sequences (including 196 newly generated) from 13 genera, 140 species, and 175 taxa across 44 countries. We find that the Western Asia (particularly the Caucasus) and the Mediterranean are the centre of origin for large clades of holoparasitic Orobancheae within the last 6 million years. In the Caucasus, the centres of diversity are composed both of long-branch taxa and shallow, recently diversified clades, while Orobancheae diversity in the Mediterranean appears to represent mainly recent diversification.
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Affiliation(s)
- Renata Piwowarczyk
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, PL-25-406 Kielce, PolandJan Kochanowski UniversityKielcePoland
| | - Adam C. Schneider
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, PL-25-406 Kielce, PolandJan Kochanowski UniversityKielcePoland
| | - Grzegorz Góralski
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Dagmara Kwolek
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Magdalena Denysenko-Bennett
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Anna Burda
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Karolina Ruraż
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, PL-25-406 Kielce, PolandJan Kochanowski UniversityKielcePoland
| | - Andrzej J. Joachimiak
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Óscar Sánchez Pedraja
- Grupo Botánico Cantábrico, ES-39722 Liérganes (Cantabria), SpainGrupo Botánico CantábricoLiérganesSpain
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4
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Ataei N, Schneeweiss GM, García MA, Krug M, Lehnert M, Valizadeh J, Quandt D. A multilocus phylogeny of the non-photosynthetic parasitic plant Cistanche (Orobanchaceae) refutes current taxonomy and identifies four major morphologically distinct clades. Mol Phylogenet Evol 2020; 151:106898. [PMID: 32585287 DOI: 10.1016/j.ympev.2020.106898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 05/24/2020] [Accepted: 06/17/2020] [Indexed: 02/09/2023]
Abstract
Phylogenetic relationships of and within non-photosynthetic parasitic lineages are notoriously poorly known, which negatively affects our understanding of parasitic plants. This is also the case for Cistanche (Orobanchaceae), an Old World genus with about two dozen species, whose relationships have not yet been addressed using molecular phylogenetic approaches. Here we infer phylogenetic relationships within the genus, employing a taxonomically and geographically broad sampling covering all previously distinguished infrageneric groups and most of the currently recognized species. A combined matrix of three plastid markers (trnL-trnF, including the trnL intron and the intergenic spacer (IGS), trnS-trnfM IGS and psbA-trnH IGS) and one nuclear marker (ITS) was analyzed using maximum parsimony, maximum likelihood and Bayesian inference. Cistanche falls into four well-supported and geographically differentiated clades: East Asian Clade, Northwest African Clade, Southwest Asian Clade and Widespread Clade. Of those, only the East Asian Clade corresponds to a previously recognized taxonomic section, whereas the others either contain members of two or three sections (Widespread Clade and Southwest Asian Clade, respectively) or have not been taxonomically recognized so far (Northwest African Clade). Whereas the Southwest Asian Clade exhibits strong phylogenetic structure among and partly within species (the East Asian Clade and the Northwest African Clade are monospecific), phylogenetic resolution within the Widespread Clade is often low and hampered by discrepancies between nuclear and plastid markers. Both molecular and morphological data indicate that species diversity in Cistanche is currently underestimated.
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Affiliation(s)
- Najibeh Ataei
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany; General Directorate for Agricultural Research Institute of Afghanistan (ARIA), Ministry of Agriculture, Irrigation and Livestock, Badam Bagh, Kabul, Afghanistan
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
| | - Miguel Angel García
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga, Canada; Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Michael Krug
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany
| | - Marcus Lehnert
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany
| | - Jafar Valizadeh
- Department of Biology, University of Sistan and Baluchistan, Zahedan, Iran
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany.
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García MA, Stefanović S, Weiner C, Olszewski M, Costea M. Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae). ORG DIVERS EVOL 2018; 18:383-398. [PMID: 30930685 PMCID: PMC6405177 DOI: 10.1007/s13127-018-0383-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023]
Abstract
As traditionally circumscribed, Cuscuta sect. Denticulatae is a group of three parasitic plant species native to the deserts of Western USA (Cuscuta denticulata, Cuscuta nevadensis) and the central region of Baja California, Mexico (Cuscuta veatchii). Molecular phylogenetic studies confirmed the monophyly of this group and suggested that the disjunct C. veatchii is a hybrid between the other two species. However, the limited sampling left the possibility of alternative biological and methodological explanations. We expanded our sampling to multiple individuals of all the species collected from across their entire geographical ranges. Sequence data from the nuclear and plastid regions were used to reconstruct the phylogeny and find out if the topological conflict was maintained. We obtained karyotype information from multiple individuals, investigated the morphological variation of the group thorough morphometric analyses, and compiled data on ecology, host range, and geographical distribution. Our results confirmed that C. veatchii is an allotetraploid. Furthermore, we found previously unknown autotetraploid population of C. denticulata, and we describe a new hybrid species, Cuscuta psorothamnensis. We suggest that this newly discovered natural hybrid is resulting from an independent (and probably more recent) hybridization event between the same diploid parental species as those of C. veatchii. All the polyploids showed host shift associated with hybridization and/or polyploidy and are found growing on hosts that are rarely or never frequented by their diploid progenitors. The great potential of this group as a model to study host shift in parasitic plants associated with recurrent allopolyploidy is discussed.
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Affiliation(s)
- Miguel A García
- 1Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6 Canada.,2Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE UK
| | - Saša Stefanović
- 1Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6 Canada
| | - Catherine Weiner
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
| | - Magdalena Olszewski
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
| | - Mihai Costea
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
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6
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Schneider AC, Chun H, Stefanović S, Baldwin BG. Punctuated plastome reduction and host-parasite horizontal gene transfer in the holoparasitic plant genus Aphyllon. Proc Biol Sci 2018; 285:rspb.2018.1535. [PMID: 30232155 DOI: 10.1098/rspb.2018.1535] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022] Open
Abstract
Foundational studies of chloroplast genome (plastome) evolution in parasitic plants have focused on broad trends across large clades, particularly among the Orobanchaceae, a species-rich and ecologically diverse family of root parasites. However, the extent to which such patterns and processes of plastome evolution, such as stepwise gene loss following the complete loss of photosynthesis (shift to holoparasitism), are detectable at shallow evolutionary time scale is largely unknown. We used genome skimming to assemble eight chloroplast genomes representing complete taxonomic sampling of Aphyllon sect. Aphyllon, a small clade within the Orobanchaceae that evolved approximately 6 Ma, long after the origin of holoparasitism. We show substantial plastome reduction occurred in the stem lineage, but subsequent change in plastome size, gene content, and structure has been relatively minimal, albeit detectable. This lends additional fine-grained support to existing models of stepwise plastome reduction in holoparasitic plants. Additionally, we report phylogenetic evidence based on an rbcL gene tree and assembled 60+ kb fragments of the Aphyllon epigalium mitochondrial genome indicating host-to-parasite horizontal gene transfers (hpHGT) of several genes originating from the plastome of an ancient Galium host into the mitochondrial genome of a recent common ancestor of A. epigalium Ecologically, this evidence of hpHGT suggests that the host-parasite associations between Galium and A. epigalium have been stable at least since its subspecies diverged hundreds of thousands of years ago.
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Affiliation(s)
- Adam C Schneider
- University and Jepson Herbaria, Berkeley, CA, USA .,Department of Integrative Biology, University of California, Berkeley, CA, USA.,Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Harold Chun
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Bruce G Baldwin
- University and Jepson Herbaria, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
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7
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Palynomorphological peculiarities of representatives of tribes Lindenbergiae and Cymbarieae and pollen evolution in early-branching lineages of Orobanchaceae. UKRAINIAN BOTANICAL JOURNAL 2018. [DOI: 10.15407/ukrbotj75.02.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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8
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Schneider AC, Moore AJ. Parallel Pleistocene amphitropical disjunctions of a parasitic plant and its host. AMERICAN JOURNAL OF BOTANY 2017; 104:1745-1755. [PMID: 29170246 DOI: 10.3732/ajb.1700181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown. METHODS Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based on the inferred timing of horizontal gene transfer from a papilionoid legume into the common ancestor of Orobanche and Phelipanche. Elevated rates of molecular evolution in the Orobanchaceae have hindered efforts to determine reliable divergence time estimates in the absence of a fossil record. However, using a horizontal gene transfer event as a secondary calibration overcomes this limitation. These chronograms were used to reconstruct the biogeography of Aphyllon, Grindelia, and relatives using a DEC+J model implemented in RevBayes. KEY RESULTS Aphyllon had two amphitropical dispersals from North America to South America, while Grindelia had a single dispersal. The dispersal of the Aphyllon lineage that is parasitic on Grindelia (0.40 Ma) took place somewhat after Grindelia began to diversify in South America (0.93 Ma). Using a secondary calibration based on horizontal gene transfer, we infer more recent divergence dates of holoparasitic Orobancheae than previous studies. CONCLUSIONS Parallel host-parasite amphitropical disjunctions in Grindelia and Aphyllon illustrate one means by which ecological specialization may result in nonindependent patterns of diversity in distantly related lineages. Although Grindelia and Aphyllon both dispersed to South America recently, Grindelia appears to have diversified more extensively following colonization. More broadly, recent Pleistocene glaciations probably have also contributed to patterns of diversity and biogeography of temperate northern hemisphere Orobancheae. We also demonstrate the utility of using horizontal gene transfer events from well-dated clades to calibrate parasite phylogenies in the absence of a fossil record.
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Affiliation(s)
- Adam C Schneider
- Department of Integrative Biology and Jepson Herbarium, 1001 Valley Life Sciences Building, University of California, Berkeley 94720 USA
| | - Abigail J Moore
- Department of Microbiology and Plant Biology and Oklahoma Biological Survey, University of Oklahoma, 770 Van Vleet Oval, Norman, Oklahoma 73019 USA
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Duca M, Port A, Boicu A, Șestacova T. Molecular Characterization of Broomrape Populations from Republic of Moldova using SSR Markers. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/helia-2017-0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe genetic diversity study of 39 broomrape populations from the Republic of Moldova was performed using 12 highly polymorphic SSR primer pairs, which shown the high level of polymorphism (average PIC value 0.57). We found that some of the SSR primers (Ocum-59 and Ocum-108) produced polymorphic bands suitable for discrimination between the studied populations. The diversity analysis within broomrape populations revealed a higher number of detected alleles and heterozygous loci in the accessions from the Southern region when compared to the Northern and Central ones. The average PIC values for the Northern, Central and Southern accessions ranged from 0.43, 0.48 to 0.56, respectively. Some populations from the Southern region (especially, Carabetovca, Alexanderfeld, Stefan-Voda and Slobozia Mare) have shown the major differences in the profiles obtained and presented the high level of genetic variability. The dendrogram based on genetic distance divided the 39 broomrape accessions into twelve clusters. High variability of
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Schneider AC. Resurrection of the genus Aphyllon for New World broomrapes (Orobanche s.l., Orobanchaceae). PHYTOKEYS 2016; 75:107-118. [PMID: 28127248 PMCID: PMC5234541 DOI: 10.3897/phytokeys.75.10473] [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: 09/12/2016] [Indexed: 06/06/2023]
Abstract
Recent phylogenetic studies support a monophyletic clade of New World broomrapes (Orobanche sects. Gymnocaulis and Nothaphyllon) sister to the Old World genus Phelipanche. I place the New World taxa in the genus Aphyllon, propose 21 new combinations, and provide a list of currently accepted taxa.
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Affiliation(s)
- Adam C. Schneider
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building, University of California, Berkeley, CA 94720-2465
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