Disentangling Reticulate Evolution of North Temperate Haplostemonous Ludwigia (Onagraceae)

While it is known that whole genome duplication (WGD) and reticulate evolution play important roles in plant evolution, the origins and evolutionary histories of most polyploid and reticulate groups are still poorly known. The North Temperate haplostemonous (NTH) Ludwigia L. (sections Isnardia (L.) W. L. Wagner & Hoch, Ludwigia, Microcarpium Munz, and Miquelia P. H. Raven) group, characterized by having 4-merous and haplostemonous flowers, pluriseriate and free seeds, glabrous and convex nectaries, and a north-temperate distribution, is a polyploid complex (2×, 4×, 6×, and 8×) of 24 species with frequent reports of inter- and intrasectional hybridization. Although earlier biosystematics studies postulated some evolutionary scenarios and recent molecular phylogenetic studies have partially tested these propositions, the full history of their reticulate evolution remains puzzling. In this study, we sequenced four chloroplast regions (rpL16, rpoB-trnC, trnL-trnF, and ycf6-psbM) and conducted extensive molecular cloning of the biparentally inherited single-copy nuclear PgiC gene (376 clones in total), sampling 23 of the 24 NTH Ludwigia species whose chromosome numbers and ploidy levels were confirmed. Both the chloroplast and PgiC trees include strongly supported sister clades of section Ludwigia (four diploid species) and the “Microcarpium complex” (composed of sections Isnardia, Microcarpium, and Miquelia), which together are sister to the rest of Ludwigia. In the PgiC tree, eight clades are identified within the Microcarpium complex, with four clades including no extant diploid species. Neither sections Isnardia nor Microcarpium are monophyletic, while the monospecific section Miquelia has a hybrid origin. By integrating our phylogenetic trees with previous cytological hypotheses, the reticulate evolution of NTH Ludwigia is disentangled and four to eight extinct diploid species are inferred. Ancestral area reconstruction supports a North American origin of L. ovalis whose current East Asian distribution reflects a relict of the Arcto-Tertiary Geoflora. Based on our results, we propose to synonymize sections Microcarpium and Miquelia under the expanded section Isnardia.

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Discordant evolution of organellar genomes in peas (Pisum L.)

10.1101/2020.05.19.104224 ◽

2020 ◽

Cited By ~ 1

Author(s):

Vera S. Bogdanova ◽

Natalia V. Shatskaya ◽

Anatoliy V. Mglinets ◽

Oleg E. Kosterin ◽

Gennadiy V. Vasiliev

Keyword(s):

Phylogenetic Trees ◽

Nuclear Genome ◽

Nuclear Gene ◽

Plant Evolution ◽

Hybrid Origin ◽

Mitochondrial Genomes ◽

North East ◽

Plastid Genomes ◽

First Time ◽

Evolutionary Fate

AbstractPlastids and mitochondria have their own small genomes which do not undergo meiotic recombination and may have evolutionary fate different from each other and nuclear genome, thus highlighting interesting phenomena in plant evolution. We for the first time sequenced mitochondrial genomes of pea (Pisum L.), in 38 accessions mostly representing diverse wild germplasm from all over pea geographical range. Six structural types of pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Bayesian phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant implying not less than six events of hybridisation of diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles is supposed to have been driven by plastid-nuclear incompatibility, known to be widespread in pea wide crosses and apparently shaping the organellar phylogenies. The topology of a phylogenetic tree based on the nucleotide sequence of a nuclear gene His5 coding for a histone H1 subtype corresponds to the current taxonomy and resembles that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin resulting from crosses of peas similar to those presently inhabiting south-east and north-east Mediterranean in broad sense.

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Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

Systematic Botany ◽

10.1600/036364408785679815 ◽

2008 ◽

Vol 33 (3) ◽

pp. 589-597 ◽

Cited By ~ 16

Author(s):

Elizabeth A. Friar ◽

Linda M. Prince ◽

Jennifer M. Cruse-Sanders ◽

Mitchell E. McGlaughlin ◽

Charles A. Butterworth ◽

...

Keyword(s):

Single Copy ◽

Nuclear Genes ◽

Hybrid Origin ◽

Internal Transcribed Spacer Region ◽

Hybrid Species ◽

Cytogenetic Data ◽

Molecular Phylogenetic ◽

Distinct Lineage ◽

Phylogenetic Hypotheses ◽

Genomic Regions

Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai'i (the Big Island).

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Phylogeny, morphology and the role of hybridization as driving force of evolution in grass tribes Aveneae and Poeae (Poaceae)

10.1101/707588 ◽

2019 ◽

Cited By ~ 1

Author(s):

Natalia Tkach ◽

Julia Schneider ◽

Elke Döring ◽

Alexandra Wölk ◽

Anne Hochbach ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Trees ◽

Morphological Evolution ◽

Morphological Characters ◽

Data Matrix ◽

Hybrid Origin ◽

Molecular Phylogenetic Analysis ◽

Study Group ◽

Ancestral State ◽

Molecular Phylogenetic

ABSTRACTTo investigate the evolutionary diversification and morphological evolution of grass supertribe Poodae (subfam. Pooideae, Poaceae) we conducted a comprehensive molecular phylogenetic analysis including representatives from most of their accepted genera. We focused on generating a DNA sequence dataset of plastid matK gene–3’trnK exon and trnL– trnF regions and nuclear ribosomal ITS1–5.8S gene–ITS2 and ETS that was taxonomically overlapping as completely as possible (altogether 257 species). The idea was to infer whether phylogenetic trees or certain clades based on plastid and nuclear DNA data correspond with each other or discord, revealing signatures of past hybridization. The datasets were analysed using maximum parsimony, maximum likelihood and Bayesian approaches. Instances of severe conflicts between the phylogenetic trees derived from both datasets, some of which have been noted earlier, unambiguously point to hybrid origin of several lineages (subtribes, groups of genera, sometimes genera) such as Phalaridinae, Scolochloinae, Sesleriinae, Torreyochloinae; Arctopoa, Castellia, Graphephorum, Hyalopodium, Lagurus, Macrobriza, Puccinellia plus Sclerochloa, Sesleria, Tricholemma, American Trisetum, etc. and presumably Airinae, Holcinae and Phleinae. ‘Calamagrostis’ flavens appears to be an intergeneric hybrid between Agrostis and Calamagrostis. Most frequently there is good agreement of other regions of the trees, apart from intrinsic different phylogenetic resolution of the respective DNA markers. To explore the to date rather unclear morphological evolution of our study group a data matrix encompassing finally 188 characters was analysed for ancestral state reconstructions (ASR) using the tree from the combined molecular dataset as presumably best approximation to the species phylogeny. For 74 characters ASRs were feasible and yielded partly surprising results for the study group as a whole but also for some of their subdivisions. Considering taxonomy and classification it became evident, that many morphological characters show a very high degree of homoplasy and are seemingly able to change within comparatively short timespans in the evolution of our grasses. Most of the taxonomic units distinguished within our study group, e.g. as subtribes, are defined less by consistent morphological characters or character combinations and should be rather understood as clades revealed by molecular phylogenetic analysis. One reason for this extreme homoplasy concerning traditionally highly rated characters of inflorescences or spikelets and their components might be that they have little to do with pollination (always wind) or adaptation to pollinators as in other angiosperms but rather with dispersal and diaspores. Easily changing structure of spikelet disarticulation, of glume, lemma or awn characters might be advantageous in the rapid adaptation to different habitats and micro-habitats, which was evidently most successfully accomplished by these grasses. A partly revised classification of Poodae is presented, including a re-instatement of tribes Aveneae and Poeae s.str. Following a comparatively narrow delineation of preferably monophyletic subtribes, Antinoriinae, Avenulinae, Brizochloinae, Helictochloinae, Hypseochloinae are described as new. New genera are Arctohyalopoa and Hyalopodium. New combinations are Arctohyalopoa lanatiflora, A. lanatiflora subsp. ivanoviae, A. lanatiflora subsp. momica, Colpodium biebersteinianum, C. kochii, C. trichopodum, C. verticillatum, Deschampsia micrathera, Dupontia fulva, Festuca masafuerana, Hyalopodium araraticum, Paracolpodium baltistanicum, Parapholis cylindrica, P. ×pauneroi. Festuca masatierrae is a new name.Supporting Information may be found online in the Supporting Information section at the end of the article.

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The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

PeerJ ◽

10.7717/peerj.4916 ◽

2018 ◽

Vol 6 ◽

pp. e4916 ◽

Cited By ~ 5

Author(s):

Narjara Lopes de Abreu ◽

Ruy José Válka Alves ◽

Sérgio Ricardo Sodré Cardoso ◽

Yann J.K. Bertrand ◽

Filipe Sousa ◽

...

Keyword(s):

Phylogenetic Trees ◽

Plastid Genome ◽

Diploid Species ◽

Distinct Species ◽

Reticulate Evolution ◽

Model Organisms ◽

Current Evidence ◽

Genomic Libraries ◽

Coding Regions ◽

Phylogenetic Implications

BackgroundCurrent evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found inPolystachyaHook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic.MethodsWe generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops).ResultsWe retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species.DiscussionOur results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions ofPolystachya concreta(Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy.Polystachya estrellensisRchb.f. can be considered a genetically distinct species fromP. concretaandP. foliosa(Lindl.) Rchb.f., but the delimitation ofP. concretaremains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.

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Molecular phylogenetic analysis of the north-temperate Labrador Teas (Ericaceae: Rhododendron Subsect. Ledum) suggests a complex genetic history

Journal of the Botanical Research Institute of Texas ◽

10.17348/jbrit.v11.i1.1138 ◽

2017 ◽

Vol 11 (1) ◽

pp. 53-65

Author(s):

Andrew Hart ◽

Kathleen Kron ◽

Emily Gillespie

Keyword(s):

Evolutionary History ◽

Sequence Data ◽

Nuclear Data ◽

Morphological Characters ◽

Hybrid Origin ◽

The North ◽

Biogeographic History ◽

Molecular Phylogenetic ◽

Vegetative Characters ◽

Floral Characters

The Labrador teas are a group of nearly circumboreal shrubs or sub-shrubs inhabiting damp habitats. The 4–7 currently recognized species are classified within Rhododendron subg. Rhododendron section Rhododendron subsect. Ledum. In floral characters, these species are extremely similar. In vegetative characters, species limits in the Labrador teas have been difficult to determine because many of the traditionally used morphological characters vary continually across the geographic range. This study investigated evolutionary history and preliminary consideration of some species boundaries in the Labrador teas using DNA sequence data from five molecular markers to generate a preliminary phylogeny of R. subsect. Ledum. Data were analyzed using Maximum Parsimony, Maximum Likelihood and Bayesian methods. The nuclear data indicate a monophyletic subsect. Ledum, but chloroplast data indicate that the North American taxa have an evolutionary history separate from the European and Asian taxa, suggesting that one or both lineages of subsect. Ledum may be of hybrid origin. Additionally, our analyses suggest that taxa combined in recent treatments (i.e. Rhododendron tomentosum) represent separate lineages and should be recognized as distinct instead of included within more broadly defined species, however our current level of sampling cannot completely resolve this issue. This study lays the groundwork for future phylogenetic studies within subsect. Ledum, illustrating the need to sample more intensively across taxa in order to capture what appears to be a complex genetic and biogeographic history.

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Reticulate evolution in the parasitic genus Cuscuta (Convolvulaceae): over and over againThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽

10.1139/b08-033 ◽

2008 ◽

Vol 86 (8) ◽

pp. 791-808 ◽

Cited By ~ 16

Author(s):

Saša Stefanović ◽

Mihai Costea

Keyword(s):

Statistical Tests ◽

Phylogenetic Analyses ◽

Nuclear Data ◽

Reticulate Evolution ◽

Hybrid Origin ◽

Closely Related Species ◽

New Mexican ◽

Molecular Phylogenetic ◽

Present Distribution ◽

Selection Of

The frequency and relative importance of hybridization in plants has been an area of intense debate. Although this evolutionary phenomenon has received considerable attention from plant biologists, there are no well-supported cases of reticulate evolution involving parasitic plants, to date. Recent molecular phylogenetic analyses revealed that the subgenus Grammica , the largest and most diverse group of the stem-parasitic genus Cuscuta (dodder), consists of 15 major clades. We describe here five cases of strongly supported discordance between phylogenies derived from plastid and nuclear data, and interpret them as results of five independent hybridization events. Three of these cases could represent relatively recent reticulations, as each of them involves more closely related species, always confined within the same major clade as their putative parental species, and are currently sympatric or parapatric with them. The two remaining cases involve species whose potential progenitors are derived from different major groups of Grammica, and which are allopatric in their present distribution. A series of statistical tests was conducted to assess and further explore the significance of this phylogenetic incongruence. Alternative explanations for discordant gene topologies are explored. Cuscuta liliputana sp. nov., a new Mexican species of hybrid origin is described.

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Karyosystematics of the Australasian stipoid grass Austrostipa and related genera: chromosome sizes, ploidy, chromosome base numbers and phylogeny

Australian Systematic Botany ◽

10.1071/sb14029 ◽

2015 ◽

Vol 28 (3) ◽

pp. 145 ◽

Cited By ~ 8

Author(s):

Grit Winterfeld ◽

Julia Schneider ◽

Hannes Becher ◽

John Dickie ◽

Martin Röser

Keyword(s):

Phylogenetic Trees ◽

Chromosome Evolution ◽

Sequence Data ◽

Base Number ◽

Chromosome Counting ◽

Metaphase Chromosomes ◽

Ploidy Levels ◽

Dna Sequence Data ◽

Molecular Phylogenetic ◽

Nuclear Its

Mitotic metaphase chromosomes were counted in 29 taxa, representing 11 subgenera of Austrostipa, and in 11 species from nine related genera of the grass subfamily Pooideae. Karyotype features were also measured. The cytogenetic data were mapped on molecular phylogenetic trees based on nuclear ITS and plastid 3ʹtrnK DNA sequence data. The trees showed four different main lineages within Austrostipa, but supported only two of the 13 acknowledged subgenera. The phylogenetic positions of the genera Anemanthele, Achnatherum, Nassella and Oloptum indicated paraphyly of the genus Austrostipa. In nuclear-sequence data, Anemanthele was nested within Austrostipa; however, in plastid-sequence data, both were sisters. The newly obtained chromosome counts in Austrostipa showed that most species have 2n = 44, the other 2n = 66. Presuming a chromosome base number of x = 11, the counts corresponded with ploidy levels of 4x and 6x respectively. Karyotype data of Austrostipa and Anemanthele were very similar. Chromosome counting in further genera suggested chromosome base numbers of x = 9, 10, 11, 12 and 13. Chromosome sizes of the phylogenetically derived tribe Stipeae were smaller than those of the earliest diverging Pooideae lineages Nardeae, Meliceae and Phaenospermateae. The mechanisms of chromosome evolution and the origin of the considerable variation in chromosome base numbers in the subfamily Pooideae are discussed in the context of chromosome evolution and biosystematics.

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Polyploidy Expands the Range of Centaurium (Gentianaceae)

Frontiers in Plant Science ◽

10.3389/fpls.2021.650551 ◽

2021 ◽

Vol 12 ◽

Author(s):

Enrique Maguilla ◽

Marcial Escudero ◽

Vania Jiménez-Lobato ◽

Zoila Díaz-Lifante ◽

Cristina Andrés-Camacho ◽

...

Keyword(s):

Mediterranean Region ◽

Nuclear Dna ◽

Western Mediterranean ◽

Ploidy Levels ◽

Ancestral Area ◽

The North ◽

Ancestral Area Reconstruction ◽

The Mediterranean ◽

Polyploidization Event ◽

High Uncertainty

The Mediterranean region is one of the most important worldwide hotspots in terms of number of species and endemism, and multiple hypotheses have been proposed to explain how diversification occurred in this area. The contribution of different traits to the diversification process has been evaluated in different groups of plants. In the case of Centaurium (Gentianaceae), a genus with a center of diversity placed in the Mediterranean region, polyploidy seems to have been an important driver of diversification as more than half of species are polyploids. Moreover, ploidy levels are strongly geographically structured across the range of the genus, with tetraploids distributed towards more temperate areas in the north and hexaploids in more arid areas towards the south. We hypothesize that the diversification processes and biodiversity patterns in Centaurium are explained by the coupled formation of polyploid lineages and the colonization of different areas. A MCC tree from BEAST2 based on three nuclear DNA regions of a total of 26 taxa (full sampling, of 18 species and 8 subspecies) was used to perform ancestral area reconstruction analysis in “BioGeoBEARS.” Chromosome evolution was analyzed in chromEvol and diversification in BAMM to estimate diversification rates. Our results suggest that two major clades diverged early from the common ancestor, one most likely in the western Mediterranean and the other in a widespread area including west and central Asia (but with high uncertainty in the exact composition of this widespread area). Most ancestral lineages in the western clade remained in or around the western Mediterranean, and dispersal to other areas (mainly northward and eastward), occurred at the tips. Contrarily, most ancestral lineages in the widespread clade had larger ancestral areas. Polyploidization events in the western clade occurred at the tips of the phylogeny (with one exception of a polyploidization event in a very shallow node) and were mainly tetraploid, while polyploidization events occurred in the widespread clade were at the tips and in an ancestral node of the phylogeny, and were mainly hexaploid. We show how ancestral diploid lineages remained in the area of origin, whereas recent and ancestral polyploidization could have facilitated colonization and establishment in other areas.

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Gene Flow between Parents with Different Ploidy Levels in a Natural Population of Leucocoryne Lindley

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.6.0833 ◽

2004 ◽

Vol 129 (6) ◽

pp. 833-835 ◽

Cited By ~ 3

Author(s):

P. Salas ◽

L. Mansur

Keyword(s):

Gene Flow ◽

Natural Population ◽

Cytological Study ◽

Plant Evolution ◽

Hybrid Origin ◽

Ploidy Levels ◽

Intermediate Phenotypes

Gene flow between species of different ploidy levels is important in plant evolution and breeding. A cytological study was conducted on a natural population with individuals belonging to the diploid L. purpurea Gay (2n = 10) and to the tetraploid L. coquimbensis F. Phil (2n = 18) species, as well as intermediate phenotypes of apparent hybrid origin. The genus Leucocoryne is endemic to Chile and it exhibits heterogeneity, presumably genetic, for shape, size, and color of its flowers. The objective of the study was to determine if there is gene flow between species having different ploidy levels. From the karyotypic analyses of the seeds, only parental types having 2n = 10 and 2n = 18 individuals were observed. However, from the bulb analyses, 2n = 10, 2n = 18, 2n = 14, and 2n = 22 individuals were encountered. The karyotypes of the 2n = 14 and 2n = 22 individuals suggest the occurrence of natural interespecific hybridization between species with different ploidy levels in nature. Models which may account for the origin of these genotypes are proposed.

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Genomic relationships among diploid and polyploid species of the genus Eryngium L. using genomic in situ hybridization

Genome ◽

10.1139/g10-071 ◽

2010 ◽

Vol 53 (10) ◽

pp. 824-831 ◽

Cited By ~ 1

Author(s):

Gisèle Yvonne Perthuy ◽

Susana Martínez ◽

Eduardo José Greizerstein ◽

Lidia Poggio

Keyword(s):

In Situ Hybridization ◽

Morphological Variability ◽

Diploid Species ◽

Genomic In Situ Hybridization ◽

Hybrid Origin ◽

Polyploid Species ◽

Ploidy Levels ◽

Close Relationship ◽

Large Genus

Eryngium L. (Umbelliferae) is a large genus including more than 250 species worldwide. The large morphological variability in this genus makes it difficult to delimit the species or to establish phylogenetic relationships. The occurrence of different ploidy levels within the genus might indicate a hybrid origin of the polyploid species. In the present study, the chromosome number and karyotype of E. regnellii are reported for the first time and the ploidy level of a population of E. paniculatum is confirmed. We compare the genomes of the diploids E. horridum and E. eburneum , the tetraploids E. megapotamicum and E. regnellii , and the hexaploids E. pandanifolium (as a representative of the whole pandanifolium complex) and E. paniculatum using genomic in situ hybridization (GISH). Although it was not possible to identify the parental species of the polyploid taxa analyzed, the GISH technique allowed us to postulate some hypotheses about their origin. Eryngium horridum and E. eburneum do not seem to be the direct progenitors of the polyploids analyzed. On the other hand, it seems that other diploid species unrelated to E. horridum and E. eburneum are involved in their origin. Our results are consistent with morphological and phylogenetic studies, indicating a close relationship between the species of the series Latifolia.

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