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Freyman WA, Johnson MG, Rothfels CJ. homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
| | - Matthew G. Johnson
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology University of California Berkeley California USA
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Crowl AA, Fritsch PW, Tiley GP, Lynch NP, Ranney TG, Ashrafi H, Manos PS. A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus). AMERICAN JOURNAL OF BOTANY 2022; 109:1596-1606. [PMID: 36109839 PMCID: PMC10286767 DOI: 10.1002/ajb2.16065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries. METHODS We used flow cytometry to verify the ploidy of putative diploid taxa and a target-enrichment approach to obtain a genomic data set for phylogenetic analyses. RESULTS Despite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of V. boreale was consistently nested in the V. myrtilloides clade and V. caesariense was nested in the V. fuscatum clade. One diploid taxon, Vaccinium pallidum, is implicated as having a homoploid hybrid origin. CONCLUSIONS This foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.
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Affiliation(s)
- Andrew A. Crowl
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNorth Carolina27607USA
- Department of BiologyDuke UniversityDurhamNorth Carolina27708USA
| | | | - George P. Tiley
- Department of BiologyDuke UniversityDurhamNorth Carolina27708USA
- Royal Botanic Gardens KewRichmondTW9 3AEUK
| | - Nathan P. Lynch
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNorth Carolina27607USA
- Department of Horticultural ScienceNorth Carolina State University, Mountain Horticultural Crops Research and Extension CenterMills RiverNorth Carolina28759USA
| | - Thomas G. Ranney
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNorth Carolina27607USA
- Department of Horticultural ScienceNorth Carolina State University, Mountain Horticultural Crops Research and Extension CenterMills RiverNorth Carolina28759USA
| | - Hamid Ashrafi
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNorth Carolina27607USA
| | - Paul S. Manos
- Department of BiologyDuke UniversityDurhamNorth Carolina27708USA
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Marshall TL, Chambers EA, Matz MV, Hillis DM. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Mol Phylogenet Evol 2021; 162:107194. [PMID: 33940060 DOI: 10.1016/j.ympev.2021.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.
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Affiliation(s)
- Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA.
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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Biodiversity and apomixis: Insights from the East-Asian holly ferns in Polystichum section Xiphopolystichum. Mol Phylogenet Evol 2018; 127:345-355. [PMID: 29763663 DOI: 10.1016/j.ympev.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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McDade LA. HYBRIDS AND PHYLOGENETIC SYSTEMATICS II. THE IMPACT OF HYBRIDS ON CLADISTIC ANALYSIS. Evolution 2017; 46:1329-1346. [DOI: 10.1111/j.1558-5646.1992.tb01127.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/1990] [Accepted: 02/05/1992] [Indexed: 11/27/2022]
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Grant PR, Grant BR. PHENOTYPIC AND GENETIC EFFECTS OF HYBRIDIZATION IN DARWIN'S FINCHES. Evolution 2017; 48:297-316. [DOI: 10.1111/j.1558-5646.1994.tb01313.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/1993] [Accepted: 04/28/1993] [Indexed: 11/29/2022]
Affiliation(s)
- Peter R. Grant
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey 08544–1003
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey 08544–1003
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Wang H, McArthur ED, Sanderson SC, Graham JH, Freeman DC. NARROW HYBRID ZONE BETWEEN TWO SUBSPECIES OF BIG SAGEBRUSH (ARTEMISIA TRIDENTATA: ASTERACEAE). IV. RECIPROCAL TRANSPLANT EXPERIMENTS. Evolution 2017; 51:95-102. [PMID: 28568779 DOI: 10.1111/j.1558-5646.1997.tb02391.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/1995] [Accepted: 08/07/1996] [Indexed: 11/28/2022]
Abstract
Does endogenous or exogenous selection stabilize the big sagebrush (Artemisia tridentata) hybrid zone? After two years of study, our reciprocal transplant experiments showed significant genotype by environment interactions for a number of fitness components, including germination, growth, and reproduction. Hybrids were the most fit within the hybrid garden. In the parental gardens, the native parental taxon was more fit than either the alien parental or hybrids. These results are consistent with the bounded hybrid superiority model, which assumes exogenous selection, but are clearly at odds with the dynamic equilibrium model, which assumes endogenous selection and universal hybrid unfitness.
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Affiliation(s)
- Han Wang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202
| | - E Durant McArthur
- USDA Forest Service, Intermountain Research Station, Shrub Sciences Laboratory, 735 North 500 East, Provo, Utah, 84606
| | - Stewart C Sanderson
- USDA Forest Service, Intermountain Research Station, Shrub Sciences Laboratory, 735 North 500 East, Provo, Utah, 84606
| | - John H Graham
- Department of Biology, Berry College, Mount Berry, Georgia, 30149
| | - D Carl Freeman
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202
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Evin A, Dobney K, Schafberg R, Owen J, Vidarsdottir US, Larson G, Cucchi T. Phenotype and animal domestication: A study of dental variation between domestic, wild, captive, hybrid and insular Sus scrofa. BMC Evol Biol 2015; 15:6. [PMID: 25648385 PMCID: PMC4328033 DOI: 10.1186/s12862-014-0269-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 12/11/2014] [Indexed: 11/24/2022] Open
Abstract
Background Identifying the phenotypic responses to domestication remains a long-standing and important question for researchers studying its early history. The great diversity in domestic animals and plants that exists today bears testament to the profound changes that domestication has induced in their ancestral wild forms over the last millennia. Domestication is a complex evolutionary process in which wild organisms are moved to new anthropogenic environments. Although modern genetics are significantly improving our understanding of domestication and breed formation, little is still known about the associated morphological changes linked to the process itself. In order to explore phenotypic variation induced by different levels of human control, we analysed the diversity of dental size, shape and allometry in modern free-living and captive wild, wild x domestic hybrid, domestic and insular Sus scrofa populations. Results We show that domestication has created completely new dental phenotypes not found in wild boar (although the amount of variation amongst domestic pigs does not exceed that found in the wild). Wild boar tooth shape also appears to be biogeographically structured, likely the result of post-glacial recolonisation history. Furthermore, distinct dental phenotypes were also observed among domestic breeds, probably the result of differing types and intensity of past and present husbandry practices. Captivity also appears to impact tooth shape. Wild x domestic hybrids possess second molars that are strictly intermediate in shape between wild boar and domestic pigs (third molars, however, showing greater shape similarity with wild boar) while their size is more similar to domestic pigs. The dental phenotypes of insular Sus scrofa populations found on Corsica and Sardinia today (originally introduced by Neolithic settlers to the islands) can be explained either by feralization of the original introduced domestic swine or that the founding population maintained a wild boar phenotype through time. Conclusions Domestication has driven significant phenotypic diversification in Sus scrofa. Captivity (environmental control), hybridization (genome admixture), and introduction to islands all correspond to differing levels of human control and may be considered different stages of the domestication process. The relatively well-known genetic evolutionary history of pigs shows a similar complexity at the phenotypic level. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0269-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allowen Evin
- Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen, UK. .,CNRS-Muséum National d'Histoire Naturelle, UMR 7209, Archéozoologie, Archéobotanique : Sociétés, Pratiques et Environnement, 55 rue Buffon, 75005, Paris, France.
| | - Keith Dobney
- Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen, UK.
| | - Renate Schafberg
- Group Animal Breeding, Institute of Agricultural and Nutritional Sciences (IANS), Martin-Luther-University Halle-Wittenberg, Theodor-Lieser-Str, 11 D-06120, Halle/Saale, Germany.
| | - Joseph Owen
- Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen, UK. .,Department of Archaeology, Simon Fraser University, Education Bulding 9635, 8888 University Dr, Burnaby, BC, V5A, Canada. .,Department of Anthropology, Durham University, South Road, Durham, DH1 3LE, UK.
| | | | - Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Thomas Cucchi
- Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen, UK. .,CNRS-Muséum National d'Histoire Naturelle, UMR 7209, Archéozoologie, Archéobotanique : Sociétés, Pratiques et Environnement, 55 rue Buffon, 75005, Paris, France.
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Soltis PS, Liu X, Marchant DB, Visger CJ, Soltis DE. Polyploidy and novelty: Gottlieb's legacy. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130351. [PMID: 24958924 PMCID: PMC4071524 DOI: 10.1098/rstb.2013.0351] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818-830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity-the production of novel enzyme forms in the allopolyploids-can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes-with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity-may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.
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Affiliation(s)
- Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Xiaoxian Liu
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
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Affiliation(s)
- David P. Mindell
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
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11
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Seberg O, Petersen G, Davis JI, Pires JC, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ, Pillon Y. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. AMERICAN JOURNAL OF BOTANY 2012; 99:875-889. [PMID: 22539521 DOI: 10.3732/ajb.1100468] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. METHODS Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. KEY RESULTS The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. CONCLUSIONS Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
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Affiliation(s)
- Ole Seberg
- Botanical Garden, Natural History Museum of Denmark, Sølvgade 83, Copenhagen K, Denmark.
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BUGGS RICHARDJA, SOLTIS PAMELAS, SOLTIS DOUGLASE. Does hybridization between divergent progenitors drive whole-genome duplication? Mol Ecol 2009; 18:3334-9. [DOI: 10.1111/j.1365-294x.2009.04285.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mouly A, Razafimandimbison SG, Khodabandeh A, Bremer B. Phylogeny and classification of the species-rich pantropical showy genus Ixora (Rubiaceae-Ixoreae) with indications of geographical monophyletic units and hybrids. AMERICAN JOURNAL OF BOTANY 2009; 96:686-706. [PMID: 21628224 DOI: 10.3732/ajb.0800235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Species-rich genera often have various conflicting circumscriptions from independent regional flora treatments. Testing the monophyly of these groups of plants is an important step toward the establishment of a phylogenetic classification. The genus Ixora of the tribe Ixoreae in the subfamily Ixoroideae (coffee family or Rubiaceae) is a species-rich pantropical genus of ca. 500 species. Phylogenetic analyses of Ixoreae based on combined sequence data from one nuclear (nrETS) and two chloroplast (rps16 and trnT-F) markers reveal the paraphyly of Ixora as presently delimited and also show that the tribe can be subdivided into three major clades: the Mascarene/neotropical/Malagasy/African clade, the Pacific clade, and the Asian clade. Given the lack of morphological synapomorphies supporting the different Ixora clades and the morphological consistency of the ingroup taxa, we propose a broad circumscription of Ixora including all its satellite genera: Captaincookia, Doricera, Hitoa, Myonima, Sideroxyloides, Thouarsiora, and Versteegia. The current infrageneric classification of Ixora is not supported. The different Ixora subclades represent geographical units. Nuclear and chloroplast tree topologies were partially incongruent, indicating at least four potential natural hybridization events. Other conflicting positions for the cultivated species are most likely due to anthropogenic hybridization.
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Affiliation(s)
- Arnaud Mouly
- UMS 2700 CNRS-USM 0602 MNHN: Taxonomie et Collections, Département de Systématique et Évolution, Muséum national d'Histoire naturelle, 16 rue Buffon 75005 Paris, France
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KELLOGG ELIZABETHA. Restriction site variation in the chloroplast genomes of the monogenomic Triticeae. Hereditas 2008. [DOI: 10.1111/j.1601-5223.1992.tb00203.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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KELLOGG ELIZABETHA. Restriction site variation in the chloroplast genomes of the monogenomic Triticeae. Hereditas 2008. [DOI: 10.1111/j.1601-5223.1992.tb00798.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Reeves PA, Richards CM. Distinguishing Terminal Monophyletic Groups from Reticulate Taxa: Performance of Phenetic, Tree-Based, and Network Procedures. Syst Biol 2007; 56:302-20. [PMID: 17464885 DOI: 10.1080/10635150701324225] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Hybridization is a well-documented, natural phenomenon that is common at low taxonomic levels in the higher plants and other groups. In spite of the obvious potential for gene flow via hybridization to cause reticulation in an evolutionary tree, analytical methods based on a strictly bifurcating model of evolution have frequently been applied to data sets containing taxa known to hybridize in nature. Using simulated data, we evaluated the relative performance of phenetic, tree-based, and network approaches for distinguishing between taxa with known reticulate history and taxa that were true terminal monophyletic groups. In all methods examined, type I error (the erroneous rejection of the null hypothesis that a taxon of interest is not monophyletic) was likely during the early stages of introgressive hybridization. We used the gradual erosion of type I error with continued gene flow as a metric for assessing relative performance. Bifurcating tree-based methods performed poorly, with highly supported, incorrect topologies appearing during some phases of the simulation. Based on our model, we estimate that many thousands of gene flow events may be required in natural systems before reticulate taxa will be reliably detected using tree-based methods of phylogeny reconstruction. We conclude that the use of standard bifurcating tree-based methods to identify terminal monophyletic groups for the purposes of defining or delimiting phylogenetic species, or for prioritizing populations for conservation purposes, is difficult to justify when gene flow between sampled taxa is possible. As an alternative, we explored the use of two network methods. Minimum spanning networks performed worse than most tree-based methods and did not yield topologies that were easily interpretable as phylogenies. The performance of NeighborNet was comparable to parsimony bootstrap analysis. NeighborNet and reverse successive weighting were capable of identifying an ephemeral signature of reticulate evolution during the early stages of introgression by revealing conflicting phylogenetic signal. However, when gene flow was topologically complex, the conflicting phylogenetic signal revealed by these methods resulted in a high probability of type II error (inferring that a monophyletic taxon has a reticulate history). Lastly, we present a novel application of an existing nonparametric clustering procedure that, when used against a density landscape derived from principal coordinate data, showed superior performance to the tree-based and network procedures tested.
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Affiliation(s)
- Patrick A Reeves
- United States Department of Agriculture, Agricultural Research Service, National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521, USA
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Shefferson RP. Survival costs of adult dormancy and the confounding influence of size in lady's slipper orchids, genus Cypripedium. OIKOS 2006. [DOI: 10.1111/j.2006.0030-1299.15231.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Smith SD, Baum DA. Phylogenetics of the florally diverse Andean clade Iochrominae (Solanaceae). AMERICAN JOURNAL OF BOTANY 2006; 93:1140-53. [PMID: 21642180 DOI: 10.3732/ajb.93.8.1140] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent molecular phylogenetic studies of Solanaceae have identified many well-supported clades within the family and have permitted the creation of a phylogenetic system of classification. Here we estimate the phylogeny for Iochrominae, a clade of Physaleae sensu Olmstead et al. (1999), which contains 34 Andean species encompassing an immense diversity of floral forms and colors. Using three nuclear regions, ITS, the second intron of LEAFY, and exons 2 to 9 of the granule-bound starch synthase gene (waxy), we evaluated the monophyly of the traditional genera comprising Iochrominae and assessed the extent of interspecific hybridization within the clade. Only one of the six traditionally recognized genera of Iochrominae was supported as monophyletic. Further, comparison of the individual nuclear data sets revealed two interspecific hybrid taxa and a third possible case. These hybrid taxa occur in the Amotape-Huancabamba zone, a region between the northern and central Andes that has the greatest diversity of Iochroma species and offers frequent opportunities for hybridization in areas of sympatry. We postulate that periodic hybridization events in this area coupled with pollinator-mediated selection and the potential for microallopatry may have acted together to promote diversification in montane Andean taxa, such as Iochrominae.
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Howarth DG, Baum DA. GENEALOGICAL EVIDENCE OF HOMOPLOID HYBRID SPECIATION IN AN ADAPTIVE RADIATION OF SCAEVOLA (GOODENIACEAE) IN THE HAWAIIAN ISLANDS. Evolution 2005. [DOI: 10.1554/03-752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Shepherd KA, Waycott M, Calladine A. Radiation of the Australian Salicornioideae (Chenopodiaceae)--based on evidence from nuclear and chloroplast DNA sequences. AMERICAN JOURNAL OF BOTANY 2004; 91:1387-1397. [PMID: 21652372 DOI: 10.3732/ajb.91.9.1387] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In phylogenetic analyses of nuclear ITS and chloroplast trnL DNA sequences, the mostly endemic Australian genera; Halosarcia, Pachycornia, Sclerostegia, Tecticornia, and Tegicornia of the subfamily Salicornioideae (Chenopodiaceae) together form a monophyletic group, congruent with the hypothesis that they evolved from a common ancestor. However, limited genetic differentiation evident in both nrDNA and cpDNA sequences among these taxa suggests a possible rapid radiation. Based on fossil pollen records and climatic models of other authors, it is hypothesized that the expansion of the Australian endemic Salicornioideae most likely occurred during the Late Miocene to Pliocene, when increasing aridity caused the formation of extensive salt lakes along endorheic paleodrainage channels. Moreover, Australian Sarcocornia representatives were supported as monophyletic, nested within a paraphyletic Sarcocornia clade that also comprised European Salicornia in the ITS analysis. This suggests that Sarcocornia arrived in Australia subsequent to the ancestor of the Australian endemic genera most likely via long-distance dispersal.
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Affiliation(s)
- K A Shepherd
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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Goldman DH, Jansen RK, van den Berg C, Leitch IJ, Fay MF, Chase MW. Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and possible hybrid speciation. AMERICAN JOURNAL OF BOTANY 2004; 91:707-723. [PMID: 21653426 DOI: 10.3732/ajb.91.5.707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The orchid genus Calopogon R.Br. (Orchidaceae), native to eastern North America and the northern Caribbean, currently contains five species and up to three varieties. Using nuclear internal transcribed spacer (ITS) ribosomal DNA sequences, amplified fragment length polymorphisms (AFLPs), chloroplast DNA restriction fragments, and chromosome counts, we present a phylogenetic and taxonomic study of the genus. Calopogon multiflorus and C. pallidus are consistently sister species, but the relationships of C. barbatus, C. oklahomensis, and C. tuberosus are not as clear. In the ITS analysis C. oklahomensis is sister to C. barbatus, whereas it is sister to C. tuberosus in the plastid restriction fragment analysis. Furthermore, all species were found to have chromosome numbers of 2n = 38 and 40, with the exception of the putatively hybrid-derived C. oklahomensis with 2n = 114 and 120. The hexaploidy of the latter, plus the discrepancy in its position between the ITS and plastid restriction fragment trees, could suggest that it is of hybrid origin. However, the presence of unique morphological and molecular characters might indicate that it is either an ancient hybrid or not of hybrid derivation at all. Finally, using these molecular methods all taxa appear to generally be discrete groups, with the exception of C. tuberosus vars. latifolius and tuberosus, the former of which is best combined with the latter.
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Affiliation(s)
- Douglas H Goldman
- Section of Integrative Biology and Plant Resources Center, University of Texas, Austin, Texas 78712 USA
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22
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Grant PR, Grant BR, Markert JA, Keller LF, Petren K. CONVERGENT EVOLUTION OF DARWIN'S FINCHES CAUSED BY INTROGRESSIVE HYBRIDIZATION AND SELECTION. Evolution 2004. [DOI: 10.1554/04-016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gross BL, Schwarzbach AE, Rieseberg LH. Origin(s) of the diploid hybrid species Helianthus deserticola (Asteraceae). AMERICAN JOURNAL OF BOTANY 2003; 90:1708-19. [PMID: 21653347 DOI: 10.3732/ajb.90.12.1708] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Homoploid hybrid speciation has traditionally been considered a rare event, dependent on the establishment of both a novel, balanced genotype and reproductive isolating barriers between the new species and its progenitors. However, more recent studies have shown that synthetic hybrids converge toward the chromosomal structure of natural hybrids after only a few generations, suggesting that this phenomenon may be more frequent than previously assumed. Here, the possibility that the diploid hybrid species Helianthus deserticola arose from more than one hybrid speciation event was investigated using patterns of variation from cpDNA, 18 nuclear microsatellite loci, and population interfertility. Helianthus deserticola contains cpDNA haplotypes characteristic of both parental species, is polyphyletic with one parental species based on nine microsatellite loci, and has a high degree of interfertility among populations. The data are consistent with either a single origin followed by introgression with the parental species or multiple origins. Analysis of microsatellite variation places the origin of H. deserticola between 170 000 and 63 000 years before present, making it unlikely that anthropogenic disturbances influenced its origin. Finally, the hybrid species generally has lower levels of genetic diversity but higher levels of differentiation among populations than either parental species.
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Affiliation(s)
- Briana L Gross
- Department of Biology, Indiana University, Jordan Hall 142, 1001 East Third Street, Bloomington, Indiana 47405 USA
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Ingram AL, Doyle JJ. The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps16. AMERICAN JOURNAL OF BOTANY 2003; 90:116-22. [PMID: 21659086 DOI: 10.3732/ajb.90.1.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Tef (Eragrostis tef; Poaceae) is an allotetraploid (2n = 4x = 40) cereal crop whose origin within the large genus Eragrostis is unknown. Previous studies have suggested a total of 14 wild Eragrostis species as potential progenitors. Phylogenetic analysis of sequence data from the nuclear gene waxy and the plastid locus rps16 strongly supports the widely held hypothesis of a close relationship between tef and E. pilosa, a wild allotetraploid. Eragrostis heteromera, another previously proposed progenitor, is shown by the waxy data to be a close relative of one of the tef genomes. Other putative progenitors included in the taxon sample are not supported as closely related to tef. Plastid sequences from five varieties of tef and four E. pilosa accessions are identical and therefore are uninformative with respect to the question of multiple origins of these polyploids. The waxy phylogeny also resolves the relationships among other allopolyploids, supporting a close relationship between the morphologically similar allotetraploids E. macilenta, E. minor, and E. mexicana. Eragrostis cilianensis, another morphologically similar allopolyploid, appears to have shared one diploid progenitor with these species but derived its other genome from an unrelated diploid.
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Affiliation(s)
- Amanda L Ingram
- Cornell University, L. H. Bailey Hortorium, 462 Mann Library, Ithaca, New York 14853 USA
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Abstract
Intraspecific gene evolution cannot always be represented by a bifurcating tree. Rather, population genealogies are often multifurcated, descendant genes coexist with persistent ancestors and recombination events produce reticulate relationships. Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account these population-level phenomena.
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Runyeon-Lager H, Prentice HC. Morphometric variation in a hybrid zone between the weed, Silene vulgaris, and the endemic, Silene uniflora ssp. petraea (Caryophyllaceae), on the Baltic island of Öland. ACTA ACUST UNITED AC 2000. [DOI: 10.1139/b00-113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
On the island of Öland the weed, Silene vulgaris (Moench) Garcke, and the endemic, Silene uniflora Roth ssp. petraea, hybridize when brought into contact by anthropogenic disturbance. Variation was studied in transects across a hybrid zone where a linear population of S. vulgaris crossed the native habitat of S. uniflora ssp. petraea. Plants were scored for 20 morphological characters. Although individual characters showed clinal trends between weed and endemic, all plants were assignable to one or other parental species. Only 14% of the 554 scored plants showed intermediacy in one or a few characters, and ordinations showed two separate groups of samples. The low number of intermediates is discussed in terms of character choice, habitat separation, disturbance history, and reproductive ecology. The results of the study are consistent with the earlier observation that the species have remained morphologically distinct on Öland, despite evidence of sparse introgression of allozymes from weed to endemic. Disturbance is necessary not only for the creation of intermediate (hybrid) habitats but also for the establishment of the weedy parent. The transient nature of S. vulgaris populations is likely to be important in limiting introgression into S. uniflora ssp. petraea under the present disturbance regime.Key words: genetic assimilation, hierarchical partitioning of diversity, habitat disturbance, introgression, rare species, clines.
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Abstract
The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of speciation and in phylogenetic reconstruction, especially when molecular data are used. As a result, hybridization has been largely treated as an evolutionary accident or statistical error in phylogenetic analysis. In this paper, I explicitly incorporate hybridization as an evolutionary occurrence and then conduct phylogenetic reconstruction. I first examine the reticulate evolution under a pure drift model, and then extend the theory to fit a mutation model. A least-squares method is developed for reconstructing a reticulate phylogeny using gene frequency data. The efficacy of the method under the pure drift model is verified via Monte Carlo simulations.
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Affiliation(s)
- S Xu
- Department of Botany and Plant Sciences, University of California at Riverside, 92521, USA.
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Giessler, Mader, Schwenk. Morphological evolution and genetic differentiation in Daphnia species complexes. J Evol Biol 1999. [DOI: 10.1046/j.1420-9101.1999.00065.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vargas P, Morton CM, Jury SL. Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences. AMERICAN JOURNAL OF BOTANY 1999. [PMID: 10330076 DOI: 10.2307/2656582] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A biogeographic study of Saxifraga section Saxifraga was performed based on phylogenetic analyses of ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. ITS sequences from 21 species and 31 populations were examined to identify colonization patterns for the two species of Saxifraga occurring in Macaronesia and for S. globulifera in the west Mediterranean basin. Phylogenetic analysis of the sequence data yield a single most parsimonious tree with many of the major clades well supported by bootstrap and decay values. The ITS tree provided resolution at specific and populational levels that points to two biogeographic patterns within the genus. In contrast to the molecular evidence provided by other authors for a Mediterranean origin of several Macaronesian genera of angiosperms, our results indicate that the Madeiran archipelago was colonized a single time by a species of Saxifraga originating from the Eurosiberian region. On the other hand, the molecular evidence also suggests that populations of S. globulifera from North Africa have been isolated for a long time from populations occurring in the Iberian Peninsula, and that the endemic S. reuteriana has evolved from the Iberian populations of S. globulifera. The Mediterranean Sea has probably been an effective isolating barrier for some plant groups that occur in Europe and North Africa.
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Affiliation(s)
- P Vargas
- Department of Botany, University of Reading, Whiteknights, P.O. Box 221, Reading RG6 2AS, UK
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Cronn RC, Zhao X, Paterson AH, Wendel JF. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 1996; 42:685-705. [PMID: 8662014 DOI: 10.1007/bf02338802] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton (Gossypium) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.
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MESH Headings
- Base Sequence
- DNA, Plant/genetics
- DNA, Ribosomal/genetics
- Diploidy
- Evolution, Molecular
- Genes, Plant
- Gossypium/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Genetic
- Polyploidy
- RNA, Plant/genetics
- RNA, Ribosomal, 5S/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Alignment
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- R C Cronn
- Department of Botany, Iowa State University, Ames, IA 50011, USA
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