Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA

This study presents a phylogeny of Zieria Sm. (Rutaceae) based on sequences of internal transcribed spacer and external transcribed spacer regions of nrDNA, and using Neobyrnesia suberosa J.A.Armstr. as the outgroup. The phylogeny includes 109 samples, representing 58 of the 60 currently recognised species of Zieria, with multiple accessions of most. Ten species were resolved as monophyletic on the basis of two, or in one case four, samples. Monophyly of four species was neither supported nor rejected, and all other species with more than one accession were resolved as polyphyletic or paraphyletic. Results showed that divergent paralogues of nrDNA are present in some individuals, although the underlying evolutionary process that gave rise to those paralogues is uncertain. Divergent paralogues within genomes could predate speciation and be variably retained or variably detected within the species sampled here; alternatively, they could represent novel nrDNA combinations formed through hybridisation after speciation. There was no strong evidence for recombination between paralogues or that paralogues represent pseudogenes. Variation of nrDNA sequences was clearly incongruent with previously published cpDNA variation, with the nrDNA potentially providing a better indication of species relationships in Zieria. Evidence for this comes from the greater level of congruence, in some species at least, between nrDNA and existing species-level taxonomy than between cpDNA and taxonomy. Incomplete lineage sorting is proposed as a plausible cause for much of the conflict between nrDNA and cpDNA in Zieria, although, in most cases, there was insufficient information to identify the underlying causes with confidence. Implications for species-level taxonomy are discussed.

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A chloroplast phylogeny of Zieria (Rutaceae) in Australia and New Caledonia shows widespread incongruence with species-level taxonomy

Australian Systematic Botany ◽

10.1071/sb14033 ◽

2014 ◽

Vol 27 (6) ◽

pp. 427 ◽

Cited By ~ 10

Author(s):

Rosemary A. Barrett ◽

Michael J. Bayly ◽

Marco F. Duretto ◽

Paul I. Forster ◽

Pauline Y. Ladiges ◽

...

Keyword(s):

Nuclear Dna ◽

New Caledonia ◽

Incomplete Lineage Sorting ◽

Species Level ◽

Lineage Sorting ◽

Widespread Species ◽

Geographic Ranges ◽

Cpdna Markers ◽

Insight Into ◽

Chloroplast Phylogeny

This study presents a molecular phylogeny of Zieria Sm., a genus of shrubs and small trees, with 59 species in Australia and one endemic to New Caledonia. The phylogeny is based on four cpDNA markers and 116 samples representing all species of Zieria except one, and the monotypic outgroup Neobyrnesia suberosa. The New Caledonian species, Z. chevalieri, was resolved as sister to a well supported clade of all Australian taxa. There was widespread incongruence between the cpDNA tree and species-level taxonomy, with 14 species shown as polyphyletic or paraphyletic. These included widespread species (e.g. Z. smithii and Z. arborescens, each falling in at least four well supported clades) and some with narrow geographic ranges (e.g. Z. alata and Z. oreocena). No species represented by three or more samples was resolved as monophyletic. We suggest that a combination of factors explains this incongruence, including regional cpDNA introgression (chloroplast capture), incomplete lineage sorting and inappropriate taxonomic boundaries. The cpDNA phylogeny provides useful insight into the evolution of Zieria but, because of its complexity, does not provide a clear basis for assessing phylogenetic relationships and monophyly of taxa. Better understanding of relationships, taxon limits and evolutionary processes in Zieria will require comparisons with nuclear DNA markers and critical assessment of morphological and genetic variation in widespread species.

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Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

PLoS ONE ◽

10.1371/journal.pone.0256126 ◽

2021 ◽

Vol 16 (8) ◽

pp. e0256126

Author(s):

Anna Victoria Silvério R. Mauad ◽

Leila do Nascimento Vieira ◽

Valter Antônio de Baura ◽

Eduardo Balsanelli ◽

Emanuel Maltempi de Souza ◽

...

Keyword(s):

Ribosomal Dna ◽

Incomplete Lineage Sorting ◽

Introgressive Hybridization ◽

Single Copy ◽

Nuclear Ribosomal Dna ◽

Molecular Characteristics ◽

Lineage Sorting ◽

Variable Regions ◽

Mutational Hotspots ◽

Phylogenomic Analyses

We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of their nuclear ribosomal DNA operon (26S, 18S, and 5.8S plus associated spacers) and partial mitochondrial genome sequences (29–38 genes and partial introns). These plastomes have the typical quadripartite structure for which gene content is similar to those of other orchids, with variation only in the composition of the ndh genes. The independent loss of ndh genes had an impact on which genes border the inverted repeats and thus the size of the small single-copy region, leading to variation in overall plastome length. Analyses of 68 coding sequences indicated the same pattern of codon usage as in other orchids, and 13 protein-coding genes under positive selection were detected. Also, we identified 62 polymorphic microsatellite loci and ten highly variable regions, for which we designed primers. Phylogenomic analyses showed that the top ten mutational hotspots represent well the phylogenetic relationships found with whole plastome sequences. However, strongly supported incongruence was observed among plastid, nuclear ribosomal DNA operon, and mitochondrial DNA trees, indicating possible occurrence of incomplete lineage sorting and/or introgressive hybridization. Despite the incongruence, the mtDNA tree retrieved some clades found in other analyses. These results, together with performance in recent studies, support a future role for mitochondrial markers in Pleurothallidinae phylogenetics.

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Bayesian phylogenetic analysis for diploid and allotetraploid species networks

10.1101/129361 ◽

2017 ◽

Cited By ~ 2

Author(s):

Graham Jones

Keyword(s):

Phylogenetic Analysis ◽

Parental Species ◽

Incomplete Lineage Sorting ◽

Reversible Jump ◽

Mcmc Algorithm ◽

Species Relationships ◽

Lineage Sorting ◽

Genome Doubling ◽

Bayesian Phylogenetic Analysis ◽

Allotetraploid Species

AbstractAllopolyploid species are formed by genome doubling after hybridization between otherwise intersterile parental species. Allopolyploidy is a common speciation mechanism in land plants. Here we describe and evaluate a Bayesian approach to the phylogenetic analysis of species relationships when both ordinary speciation and allopolyploidy are present. The approach takes incomplete lineage sorting into account using the multi-species coalescent model, and extends this to deal with the extra complications due to allopolyploidy. The number of hybridizations is not assumed, which means that the number of parameters varies and a reversible-jump MCMC algorithm is needed to sample from the posterior. The main restriction is that only diploids and allotetraploids are considered. The model is implemented in the BEAST framework and is an extension of Jones et al. (2013). Simulations show that the topology of the network can be reliably inferred along with estimates of other parameters.

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Species-level phylogeny of Allium subgenus Melanocrommyum : Incomplete lineage sorting, hybridization and trnF gene duplication

Taxon ◽

10.1002/tax.593012 ◽

2010 ◽

Vol 59 (3) ◽

pp. 829-840 ◽

Cited By ~ 33

Author(s):

Maia Gurushidze ◽

Reinhard M. Fritsch ◽

Frank R. Blattner

Keyword(s):

Gene Duplication ◽

Incomplete Lineage Sorting ◽

Species Level ◽

Lineage Sorting

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Multilocus inference of species trees and DNA barcoding

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0335 ◽

2016 ◽

Vol 371 (1702) ◽

pp. 20150335 ◽

Cited By ~ 36

Author(s):

Diego Mallo ◽

David Posada

Keyword(s):

Dna Barcoding ◽

Statistical Power ◽

Incomplete Lineage Sorting ◽

Gene Tree ◽

Evolutionary Process ◽

Species Tree ◽

Species Trees ◽

Lineage Sorting ◽

Advantages And Disadvantages ◽

Stochastic Error

The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’.

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Molecular evidence for reticulate speciation in Astragalus (Fabaceae) as revealed by a case study from sect. Dissitiflori

Botany ◽

10.1139/cjb-2013-0036 ◽

2013 ◽

Vol 91 (10) ◽

pp. 702-714 ◽

Cited By ~ 10

Author(s):

László Bartha ◽

Nicolae Dragoş ◽

Attila Molnár V. ◽

Gábor Sramkó

Keyword(s):

Incomplete Lineage Sorting ◽

Phylogenetic Network ◽

Evolutionary Process ◽

Its Region ◽

Molecular Evidence ◽

Nrdna Its ◽

Lineage Sorting ◽

Ancestral Polymorphism ◽

Shed Light

Although hybridization has long been recognized as a major force driving speciation in land plants, it has not yet been evidenced in Astragalus, the largest angiosperm genus. Here, we reveal the possible contribution of hybridization to speciation in Astragalus by employing cloning of the nrDNA ITS region and sampling three plastid regions (ycf1, ndhF–rpl32, and rpl32–trnL) in taxa belonging to sect. Dissitiflori. Phylogenetic network and tree analyses uncovered various levels of intra-individual and intraspecific polymorphism of ITS in most of the taxa investigated. Two distantly related ribotype groups were found to be shared by the closely related polyploids Astragalus pallescens M.Bieb., Astragalus peterfii Jáv., and Astragalus pseudoglaucus Klokov suggesting ancient hybridization followed by incomplete lineage sorting (i.e., shared ancestral polymorphism) in nrDNA ITS. Reticulation is also invoked as an underlying evolutionary process behind the statistically highly supported incongruent placement of A. pseudoglaucus and Astragalus vesicarius subsp. pastellianus (Pollini) Arcang. in nuclear versus plastid phylogenies. The phylogenetic results also shed light on taxonomic controversies in the section, such as the false synonimization of A. peterfii under A. vesicarius s.l. Our results provide evidence for the (at least past) existence of speciation processes driven by hybridization in Astragalus.

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Genetic diversity and species delimitation of the zeorin-containing red-fruitedCladoniaspecies (lichenized Ascomycota) assessed with ITS rDNA and β-tubulin data

The Lichenologist ◽

10.1017/s0024282913000297 ◽

2013 ◽

Vol 45 (5) ◽

pp. 665-684 ◽

Cited By ~ 15

Author(s):

Jana STEINOVÁ ◽

Soili STENROOS ◽

Martin GRUBE ◽

Pavel ŠKALOUD

Keyword(s):

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Nuclear Ribosomal Dna ◽

Lineage Sorting ◽

Evolutionary Mechanisms ◽

Phylogenetic Discordance ◽

Secondary Substances ◽

Morphological Species ◽

Β Tubulin

AbstractZeorin-containing red-fruitedCladoniaspecies, the so-calledC. cocciferagroup, are widespread terrestrial lichens which share most of their secondary substances but differ morphologically. The main objective of this study was to explore whether the current delimitation of these species is supported by molecular data. A total of 52 European and North American specimens ofC. coccifera,C. deformis,C. diversa, andC. pleurotawere examined. The internal transcribed spacer regions of the nuclear ribosomal DNA and the β-tubulin gene loci were sequenced for phylogenetic analyses. Traditional morphological species circumscriptions in zeorin-containing members of theC. cocciferagroup are not supported by molecular data.Cladonia coccifera,C. deformis, andC. pleurotawere recovered as polyphyletic in both gene topologies;C. diversaformed a lineage in the ITS phylogeny but this was not statistically supported. We detected chemical patterns of the presence/absence of porphyrilic and/or isousnic acid which may help to characterize two lineages. Our results also show incongruence between the two molecular markers studied. Therefore, we focused on possible explanations of this phenomenon. Five major evolutionary mechanisms can potentially result in phylogenetic discordance between genes: presence of pseudogenes, horizontal gene transfer, gene paralogy, incomplete lineage sorting, and hybridization. These mechanisms are briefly discussed. We consider incomplete lineage sorting and/or hybridization to best explain the incongruence.

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Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

Frontiers in Plant Science ◽

10.3389/fpls.2021.720171 ◽

2022 ◽

Vol 12 ◽

Author(s):

Chia-Lun Hsieh ◽

Chih-Chieh Yu ◽

Yu-Lan Huang ◽

Kuo-Fang Chung

Keyword(s):

Incomplete Lineage Sorting ◽

Divergence Time ◽

Time Estimation ◽

Nuclear Ribosomal Dna ◽

Length Variation ◽

Lineage Sorting ◽

Divergence Time Estimation ◽

Generic Delimitation ◽

History Of

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

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Speciation genes are more likely to have discordant gene trees

10.1101/244822 ◽

2018 ◽

Cited By ~ 1

Author(s):

Richard J. Wang ◽

Matthew W. Hahn

Keyword(s):

Gene Flow ◽

Reproductive Isolation ◽

Incomplete Lineage Sorting ◽

Gene Trees ◽

Species Trees ◽

Species Relationships ◽

Lineage Sorting ◽

Epistatic Interactions ◽

Speciation Event ◽

History Of

AbstractSpeciation genes are responsible for reproductive isolation between species. By directly participating in the process of speciation, the genealogies of isolating loci have been thought to more faithfully represent species trees. The unique properties of speciation genes may provide valuable evolutionary insights and help determine the true history of species divergence. Here, we formally analyze whether genealogies from loci participating in Dobzhansky-Muller (DM) incompatibilities are more likely to be concordant with the species tree under incomplete lineage sorting (ILS). Individual loci differ stochastically from the true history of divergence with a predictable frequency due to ILS, and these expectations—combined with the DM model of intrinsic reproductive isolation from epistatic interactions—can be used to examine the probability of concordance at isolating loci. Contrary to existing verbal models, we find that reproductively isolating loci that follow the DM model are often more likely to have discordant gene trees. These results are dependent on the pattern of isolation observed between three species, the time between speciation events, and the time since the last speciation event. Results supporting a higher probability of discordance are found for both derived-derived and derived-ancestral DM pairs, and regardless of whether incompatibilities are allowed or prohibited from segregating in the same population. Our overall results suggest that DM loci are unlikely to be especially useful for reconstructing species relationships, even in the presence of gene flow between incipient species, and may in fact be positively misleading.

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Exploring Evolutionary Dynamics of nrDNA in Carex Subgenus Vignea (Cyperaceae)

Systematic Botany ◽

10.1600/036364408785679860 ◽

2008 ◽

Vol 33 (3) ◽

pp. 514-524 ◽

Cited By ~ 16

Author(s):

Matthew G. King ◽

Eric H. Roalson

Keyword(s):

Concerted Evolution ◽

Evolutionary Dynamics ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Ribosomal Subunit ◽

Nuclear Ribosomal Dna ◽

Phylogeny Reconstruction ◽

Lineage Sorting ◽

Future Studies ◽

Carex Subgenus Vignea

Nuclear ribosomal DNA (nrDNA) has been used for more than a decade in species level phylogenetic analyses. While nrDNA can often be a powerful phylogenetic marker, intraindividual polymorphisms of the internal and external transcribed spacers (ITS, ETS) can lead to problems in their use for phylogeny reconstruction. Incomplete concerted evolution coupled with hybridization and incomplete lineage sorting can further exacerbate these problems. Previous phylogenetic analyses using nrDNA of Carex subgenus Vignea suggest that the current sectional classifications may be highly artificial. We endeavored to identify what influence incomplete concerted evolution, lineage sorting, and hybridization have played in the complex patterns of relationships previously inferred from ITS and ETS sequences for subgenus Vignea. Through comprehensive cloning we identified high levels of intraindividual polymorphisms and in many cases this led to the polyphyly of individuals. Furthermore, individuals identified with novel mutations in the 5.8S ribosomal subunit did not show a significant deviation in G-C percentage and free energy. Based on these results we suggest that nrDNA contains multiple paralogs in many species and clades within Carex subgenus Vignea which greatly complicates its use for phylogenetic inference of relationships and future studies in Carex need to take this into account.

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