scholarly journals Testing hypotheses of hybrid origins for two seashore species of Carex section Phacocystis (Cyperaceae)

2020 ◽  
Vol 194 (1) ◽  
pp. 100-117
Author(s):  
Michael D Nowak ◽  
A Tiril M Pedersen ◽  
Anne K Brysting ◽  
Audun Schrøder-Nielsen ◽  
Reidar Elven ◽  
...  
Keyword(s):  
Clonal Propagation ◽  
Parental Species ◽  
Sequence Data ◽  
Genomic Data ◽  
Putative Hybrid ◽  
Genetic Structuring ◽  
Hybrid Species ◽  
Testing Hypotheses ◽  
Future Studies ◽  
Analytical Approaches

Abstract Taxonomists have proposed numerous hybrid species in plants, but to gain a better understanding of the role that hybridization may play in plant diversification, such taxonomic hypotheses must be tested using genomic data. In this study, we employ ddRAD sequence data to test taxonomic hypotheses of hybrid origins in Carex salina and C. ramenskii (Carex section Phacocystis). Sequence data from multiple Norwegian and Icelandic populations of the putative hybrid and parental species were generated for hundreds of ddRAD loci. These data were used to estimate geographical structuring of genetic diversity and admixture and to explicitly test for hybrid origins using several analytical approaches. Our results indicate recurrent hybrid origins for the populations of C. salina and C. ramenskii sampled in our study and show that these populations are characterized by high interspecific heterozygosity. Our results support the idea that hybridization may indeed play an important role in the diversification of lineages of Carex and highlight the important role that clonal propagation might play in maintaining hybrid populations. Future studies focusing on a broader geographical sampling would be needed to assess if the genetic structuring in these Nordic populations reflects range-wide patterns in these hybrid lineages.

scholarly journals A new hybrid from Taiwan, Elatostema ×hybrida (Urticaceae), is the first confirmed natural hybrid for Urticaceae

Phytotaxa ◽  
2014 ◽  
Vol 161 (1) ◽  
pp. 43 ◽  
Author(s):  
Yu-Hsin Tseng ◽  
Jer-Ming Hu
Keyword(s):  
Sequence Data ◽  
Pollen Viability ◽  
Pollen Dispersal ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Natural Hybridization ◽  
Putative Hybrid ◽  
Natural Hybrid ◽  
Hybrid Species ◽  
Dna Sequence Data

Explosive pollen dispersal is common in Urticaceae and they are thought to be wind-pollinated. Despite a lack of obvious mechanism for preventing cross-species pollination, putative hybrid species in Urticaceae are rarely documented. Here we described the first natural hybrid in Urticaceae Elatostema ×hybrida from Taiwan. Morphological characters in E. ×hybrida are intermediate between putative parental species: E. lineolatum var. majus and E. platyphylloides. Six hybrid populations of E. ×hybrida were found in Taiwan that exhibited largely overlapping distribution patterns with its putative parents. Phylogenetic analysis of chloroplast DNA showed that the hybrid species is more closely related to E. lineolatum var. majus suggesting that the latter is the maternal parent and that hybridization is unidirectional. The chromosome number of E. ×hybrida remains the same as its putative parents (2n = 26). We speculate that the examined hybrids are natural first-generation results of independent hybridization events. Based on the morphology, spatial distribution, DNA sequence data, pollen viability and cytological observations, we hypothesize that E. ×hybrida is derived from natural hybridization events between E. lineolatum var. majus (♀) and E. platyphylloides (♂).

scholarly journals An Invariants-based Method for Efficient Identification of Hybrid Species From Large-scale Genomic Data

2015 ◽  
Author(s):  
Laura Kubatko ◽  
Julia Chifman
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Simulated Data ◽  
Species Tree ◽  
Computational Time ◽  
Putative Hybrid ◽  
Hybrid Speciation ◽  
Unified Framework ◽  
Hybrid Species ◽  
Genome Scale

Coalescent-based species tree inference has become widely used in the analysis of genome-scale multilocus and SNP datasets when the goal is inference of a species-level phylogeny. However, numerous evolutionary processes are known to violate the assumptions of a coalescence-only model and complicate inference of the species tree. One such process is hybrid speciation, in which a species shares its ancestry with two distinct species. Although many methods have been proposed to detect hybrid speciation, only a few have considered both hybridization and coalescence in a unified framework, and these are generally limited to the setting in which putative hybrid species must be identified in advance. Here we propose a method that can examine genome-scale data for a large number of taxa and detect those taxa that may have arisen via hybridization, as well as their potential ``parental'' taxa. The method is based on a model that considers both coalescence and hybridization together, and uses phylogenetic invariants to construct a test that scales well in terms of computational time for both the number of taxa and the amount of sequence data. We test the method using simulated data for up 20 taxa and 100,000bp, and find that the method accurately identifies both recent and ancient hybrid species in less than 30 seconds. We apply the method to two empirical datasets, one composed ofSistrurusrattlesnakes for which hybrid speciation is not supported by previous work, and one consisting of several species ofHeliconiusbutterflies for which some evidence of hybrid speciation has been previously found.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

New varieties of Diphasiastrum zeilleri (Rouy) Holub (Lycopodiaceae)

2016 ◽  
pp. 5-21
Author(s):  
Yu. A. Ivanenko
Keyword(s):  
Parental Species ◽  
Introgressive Hybridization ◽  
Growing Season ◽  
High Variability ◽  
Separate Species ◽  
New Variety ◽  
Hybrid Species ◽  
New Varieties ◽  
Light And Shadow ◽  
Ecological Forms

Diphasiastrum zeilleri (Rouy) Holub is a hybrid species, with the formula D. complanatum (L.) Holub × D. tristachyum (Pursh) Holub. A high variability of D. zeilleri is due to environmental conditions (light and shadow ecological forms) and probably to introgressive hybridization with the parental species. Intermediate forms between D. zeilleri, D. complanatum and D. tristachyum are quite rare, that allows to treat the three taxa as separate species. D. zeilleri is missing in subarctic regions of Europe and North America, and some degree of its resemblance with D. complanatum subsp. montellii Kukk. is convergent. Lycopodium complanatum f. polystachyum H. Lindb. is considered to belong to D. zeilleri, and an appropriate conbination is published, Diphasiastrum zeilleri var. polystachyum (H. Lindb.) Ivanenko. A new variety Diphasiastrum zeilleri (Rouy) Holub var. ramistachyum Ivanenko is described, differing by sessile strobili formed on the basal part of fertile branches during one growing season. The structure, the base of which is a fertile branch, and the upper part is strobilus (strobili), is proposed to term «strobilus branch». Besides D. zeilleri var. ramistachyum, the strobilus branches are produced by D. issleri (Rouy) Holub, D. oellgaardii Stoor, Boudrie, Jérôme, K. Horn et Bennert, and rarely by D. alpinum (L.) Holub and D. complanatum.

scholarly journals Molecular differentiation of the Murraya paniculata Complex (Rutaceae: Aurantioideae: Aurantieae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Chung Huy Nguyen ◽  
G. Andrew C. Beattie ◽  
Anthony M. Haigh ◽  
Inggit Puji Astuti ◽  
David J. Mabberley ◽  
...  
Keyword(s):  
Sequence Data ◽  
Its Region ◽  
Molecular Dating ◽  
Putative Hybrid ◽  
Citrus Industry ◽  
Morphological Studies ◽  
Murraya Paniculata ◽  
Taxonomic Uncertainty ◽  
Liberibacter Asiaticus ◽  
Cryptic Taxa

Abstract Background Orange jasmine has a complex nomenclatural history and is now known as Murraya paniculata (L.) Jack. Our interest in this common ornamental stemmed from the need to resolve its identity and the identities of closely related taxa as hosts of the pathogen ‘Candidatus Liberibacter asiaticus’ and its vector Diaphorina citri. Understanding these microbe-vector-plant relationships has been hampered by taxonomic confusion surrounding Murraya at both the generic and specific levels. Results To resolve the taxonomic uncertainty, six regions of the maternally-inherited chloroplastal genome and part of the nuclear-encoded ITS region were amplified from 85 accessions of Murraya and Merrillia using the polymerase chain reaction (PCR). Clustering used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI). Chronograms were produced for molecular dating, and to test the monophyly of Murraya rigorously, using selected accessions of Murraya and 26 accessions of the Rutaceae and Simarubaceae. Sequence data from the ITS and chloroplastal regions suggest that Murraya paniculata (sensu (Swingle WT and Reece CR, The Citrus Industry, p. 190–430, 1967)) can be separated into four distinct but morphologically somewhat cryptic taxa: Murraya paniculata (sensu (Mabberley DJ, Taxon 65:366–371, 2016)), M. elongata, M. sumatrana and M. lucida. In addition, Murraya omphalocarpa was identified as a putative hybrid of M. paniculata and M. lucida with two geographically isolated nothovarieties representing reciprocal crosses. Murraya is monophyletic, and molecular dating suggests that it diverged from Merrillia during the Miocene (23–5 Ma) with this Murraya group speciating and dispersing during the Middle Miocene onwards. Conclusions The accessions from Asia and Australasia used in this study grouped into biogeographical regions that match herbarium specimen records for the taxa that suggest natural allopatric distributions with limited overlap and hybridity. Murraya paniculata has been distributed around the world as an ornamental plant. The division of the Murraya paniculata complex into four species with a rare hybrid also confirms morphological studies.

scholarly journals Chromosomal Pairing and Pollen Viability in Rhizophora mangle and Rhizophora stylosa Hybrids

2002 ◽  
Vol 20 (1) ◽  
pp. 1 ◽  
Author(s):  
Anand P. Tyagi
Keyword(s):  
Diploid Number ◽  
Parental Species ◽  
Pollen Viability ◽  
Rhizophora Mangle ◽  
Staining Technique ◽  
Putative Hybrid ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Chromosomal Pairing ◽  
Very High

Two prominent mangrove species of Fiji, Rhizophora mangle, Linn. Rhizophora stylosa Griff and their puative hyubrid (R x selala) were analysed for chromosome number and pairing. Both parental species and their hybrid possess a diploid number of (2n) = 36 chromosomes. Regular 18 bivalents were observed in two species but the hybrid lacked proper chromosome pairing during meiosis. Analysis of tetrads showed normal tetrad and microspores development in parental species but very high abnormality in the hybrid. Pollen fertility determined by staining technique and pollen germination technique showed very high pollen viability in both parental species but very low pollen viability in the putative hybrid. Lack of chromosomal homology appears to be contributing to high percentage of non-viable pollen resulting in complete sterility in the putative hybrid.

scholarly journals HiCUP: pipeline for mapping and processing Hi-C data

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1310 ◽  
Author(s):  
Steven W. Wingett ◽  
Philip Ewels ◽  
Mayra Furlan-Magaril ◽  
Takashi Nagano ◽  
Stefan Schoenfelder ◽  
...  
Keyword(s):  
Quality Control ◽  
Reference Genome ◽  
Sequence Data ◽  
Three Dimensional ◽  
Future Studies ◽  
Processing Sequence ◽  
Experimental Protocols ◽  
Genomic Organisation

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies.

Phylogeny of the Parmeliaceae–DNA Data Versus Morphological Data

1998 ◽  
Vol 30 (4-5) ◽  
pp. 463-472 ◽  
Author(s):  
Jan-Eric Mattsson ◽  
Mats Wedin
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Slight Variation ◽  
Hypogymnia Physodes ◽  
Nuclear Rdna ◽  
Future Studies ◽  
The Family ◽  
Rdna Sequence Data ◽  
Close Relationship

AbstractIn order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

scholarly journals Reproductive isolation of hybrid populations driven by genetic incompatibilities

2014 ◽  
Author(s):  
Molly Schumer ◽  
Rongfeng Cui ◽  
Gil G Rosenthal ◽  
Peter Andolfatto
Keyword(s):  
Reproductive Isolation ◽  
Alternative Model ◽  
Parental Species ◽  
Small Population ◽  
Hybrid Population ◽  
Ecological Niches ◽  
Simple Consequence ◽  
Hybrid Species ◽  
Population Sizes ◽  
Adaptive Radiations

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. A key feature of these models is that these novel phenotypes ecologically isolate hybrid populations from parental populations, precipitating speciation. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against incompatibilities. Unlike previous models, our model does not require small population sizes, the availability of new niches for hybrids or ecological or sexual selection on hybrid traits. We show that reproductive isolation between hybrids and parents evolves frequently and rapidly under this model, even in the presence of ongoing migration with parental species and strong selection against hybrids. Our model predicts that multiple distinct hybrid species can emerge from replicate hybrid populations formed from the same parental species, potentially generating patterns of species diversity and relatedness that mimic adaptive radiations.

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