Interspecific hybridization in North American Polygala (Polygalaceae)

As a part of ongoing systematic and phylogenetic studies in Polygalaceae, field collections of two pairs of North American species (Polygala balduinii and P. ramosa, and P. lutea and P. rugelii) had morphologically intermediate forms and grew sympatrically, and so were suspected to be interspecific hybrids. Although hybrids among plants are often invoked in taxonomic and floristic literature based on morphologic intermediacy, they are rarely documented and substantiated using molecular tools. We found that the morphologically intermediate individuals within intermixed populations of both species pairs did indeed share all of the variable nucleotide sites in nrITS among the parent species. Likewise, using plastid sequence data (trnL-F), we determined that in both species pairs, the parentage was bidirectional. Although some DNA inheritance phenomena (e.g. incomplete lineage sorting) can result in similar polymorphic DNA sequence data, the intermediacy in both morphology and sequence data within sympatric populations is more indicative of interspecific hybridization.

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Phylogeny, biogeography and foliar manganese accumulation of Gossia (Myrtaceae)

Australian Systematic Botany ◽

10.1071/sb18018 ◽

2018 ◽

Cited By ~ 1

Author(s):

Todd McLay ◽

Gareth D. Holmes ◽

Paul I. Forster ◽

Susan E. Hoebee ◽

Denise R. Fernando

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

Phylogenetic Position ◽

Strongly Correlated ◽

Lineage Sorting ◽

Dna Sequence Data ◽

Australian Species ◽

Wide Range ◽

Single Clade ◽

The Relationship

The rainforest genus Gossia N.Snow & Guymer (Myrtaceae) occurs in Australia, Melanesia and Malesia, and is capable of hyperaccumulating the heavy metal manganese (Mn). Here, we used nuclear ribosomal and plastid spacer DNA-sequence data to reconstruct the phylogeny of 19 Australian species of Gossia and eight New Caledonian taxa. Our results indicated that the relationship between Gossia and Austromyrtus (Nied.) Burret is not fully resolved, and most Australian species were supported as monophyletic. Non-monophyly might be related to incomplete lineage sorting or inaccurate taxonomic classification. Bark type appears to be a morphological synapomorphy separating two groups of species, with more recently derived lineages having smooth and mottled ‘python’ bark. New Caledonian species were well resolved in a single clade, but were not the first diverging Gossia lineage, calling into doubt the results of a recent study that found Zealandia as the ancestral area of tribe Myrteae. Within Australia, the evolution of multiple clades has probably been driven by well-known biogeographic barriers. Some species with more widespread distributions have been able to cross these barriers by having a wide range of soil-substrate tolerances. Novel Mn-hyperaccumulating species were identified, and, although Mn hyperaccumulation was not strongly correlated with phylogenetic position, there appeared to be some difference in accumulation levels among clades. Our study is the first detailed phylogenetic investigation of Gossia and will serve as a reference for future studies seeking to understand the origin and extent of hyperaccumulation within the Myrteae and Myrtaceae more broadly.

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Nomenclatural Changes in Western North American Amsinckiinae (Boraginaceae)

Novon A Journal for Botanical Nomenclature ◽

10.3417/2019469 ◽

2020 ◽

Vol 28 (1) ◽

pp. 51-59

Author(s):

C. Matt Guilliams ◽

Kristen E. Hasenstab-Lehman ◽

Bruce G. Baldwin

Keyword(s):

Dna Sequence ◽

North American ◽

New Genus ◽

Sequence Data ◽

New Combination ◽

Evolutionary Relationships ◽

Dna Sequence Data ◽

Phylogenetic Studies

Three recent phylogenetic studies have used DNA sequence data to examine evolutionary relationships in Amsinckiinae (Boraginaceae). In each of these studies, the genus Plagiobothrys Fisch. & C. A. Mey. has been recovered as non-monophyletic. So that only monophyletic groups are recognized, two new genus names are provided here: Amsinckiopsis (I. M. Johnst.) Guilliams, Hasenstab & B. G. Baldwin and Simpsonanthus Guilliams, Hasenstab & B. G. Baldwin. The new combination P. collinus (Phil.) I. M. Johnst. var. pringlei (Greene) Guilliams & B. G. Baldwin is given for plants from Arizona that were found to be phylogenetically nested within P. collinus. The genus name Sonnea Greene is lectotypified.

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Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data

Phytotaxa ◽

10.11646/phytotaxa.429.3.6 ◽

2020 ◽

Vol 429 (3) ◽

pp. 239-247

Author(s):

NIGEL P. BARKER ◽

TAMIKA FELLOWS ◽

NTOMBIFIKILE PHALISO ◽

JOHN ROURKE

Keyword(s):

Genetic Diversity ◽

Bayesian Analysis ◽

Southern Africa ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Summer Rainfall ◽

Coastal Forests ◽

Lineage Sorting ◽

Dna Sequence Data ◽

Cpdna Sequence

Veltheimia is a genus of two species of bulbous flowering angiosperms restricted to southern Africa. Both parsimony and Bayesian analysis of 1829 nucleotides of DNA sequence data, from three non-coding chloroplast regions from multiple samples of both species, indicates that specimens of V. bracteata form a monophyletic clade together with three specimens named as V. capensis. This clade receives low support and is embedded within a paraphyletic grade of specimens of V. capensis. A Median Joining Network analysis of a subset of samples revealed nine haplotypes, the relationships of which mirrored the relationships resolved by the Bayesian analysis. With the exception of the V. capensis members of the V. bracteata clade, the remaining specimens are from the summer rainfall thicket and coastal forests. The samples of the basal V. capensis grade are found in the winter rainfall regions of southern Africa. These results indicate that there is limited genetic diversity within the genus, and there is no clear distinction between these two species based on plastid non-coding DNA data. This may be due to their recent divergence and incomplete lineage sorting, or recent or ongoing hybridisation and / or introgression.

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The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)

10.1101/2020.05.19.103598 ◽

2020 ◽

Cited By ~ 2

Author(s):

Bradley T. Martin ◽

Tyler K. Chafin ◽

Marlis R. Douglas ◽

John S. Placyk ◽

Roger D. Birkhead ◽

...

Keyword(s):

Machine Learning ◽

North American ◽

Species Delimitation ◽

Species Concept ◽

Incomplete Lineage Sorting ◽

Signal To Noise Ratio ◽

Lineage Sorting ◽

Biogeographic History ◽

Box Turtles ◽

A Minor

AbstractModel-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (Terrapene spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.

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

10.7287/peerj.preprints.27614 ◽

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.

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Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

Zootaxa ◽

10.11646/zootaxa.4750.3.2 ◽

2020 ◽

Vol 4750 (3) ◽

pp. 328-348 ◽

Cited By ~ 2

Author(s):

DAVID A. GRAY ◽

DAVID B. WEISSMAN ◽

JEFFREY A. COLE ◽

EMILY MORIARTY LEMMON

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

The United States ◽

Field Cricket ◽

Future Research ◽

Gene Trees ◽

Lineage Sorting ◽

The Bahamas ◽

Field Crickets ◽

Anchored Hybrid Enrichment

We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence data and Astral analysis of gene trees gave broadly congruent results, especially for older branches and overall tree structure. The North American Gryllus are monophyletic with respect to the two Old World taxa; certain sub-groups show rapid recent divergence. This is the first Anchored Hybrid Enrichment study of an insect group done for closely related species within a single genus, and the results illustrate the challenges of reconstructing the evolutionary history of young rapidly diverged taxa when both incomplete lineage sorting and probable hybridization are at play. Because Gryllus field crickets have been used extensively as a model system in evolutionary ecology, behavior, neuro-physiology, speciation, and life-history and life-cycle evolution, these results will help inform, interpret, and guide future research in these areas.

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A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

Molecular Biology and Evolution ◽

10.1093/molbev/msz296 ◽

2019 ◽

Vol 37 (4) ◽

pp. 1211-1223 ◽

Cited By ~ 8

Author(s):

Tomáš Flouri ◽

Xiyun Jiao ◽

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Gene Flow ◽

Genomic Sequence ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Mosquito Species ◽

Phylogenomic Analysis ◽

Data Sets ◽

Lineage Sorting ◽

Coalescent Model ◽

Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

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Use of nuclear genes for phylogeny reconstruction in plants

Australian Systematic Botany ◽

10.1071/sb03015 ◽

2004 ◽

Vol 17 (2) ◽

pp. 145 ◽

Cited By ~ 246

Author(s):

Randall L. Small ◽

Richard C. Cronn ◽

Jonathan F. Wendel

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Nuclear Genes ◽

Universal Primers ◽

Plant Systematics ◽

Dna Sequence Data ◽

Rdna Sequences ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Orthologous Loci

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.

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A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

10.1101/766741 ◽

2019 ◽

Cited By ~ 1

Author(s):

Thomas Flouris ◽

Xiyun Jiao ◽

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Gene Flow ◽

Genomic Sequence ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Mosquito Species ◽

Genomic Analysis ◽

Comparative Genomic ◽

Lineage Sorting ◽

Multispecies Coalescent ◽

Important Means

AbstractRecent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

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

PeerJ ◽

10.7717/peerj.7178 ◽

2019 ◽

Vol 7 ◽

pp. e7178 ◽

Cited By ~ 1

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, mitochondrion; 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 or the presence of co-dominance, 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.

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